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lars20070/QualityControl_20151104.toppas

Created November 4, 2015 12:51
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Quality Control workflow, 4/11/2015
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QualityControl_20151104.toppas
<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="info" description="">
<ITEM name="version" value="2.0.0" type="string" description="" required="false" advanced="false" />
<ITEM name="num_vertices" value="21" type="int" description="" required="false" advanced="false" />
<ITEM name="num_edges" value="27" type="int" description="" required="false" advanced="false" />
<ITEM name="description" value="&lt;![CDATA[&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt; &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt; p, li { white-space: pre-wrap; } &lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:&apos;Arial&apos;; font-size:12pt; font-weight:400; font-style:normal;&quot;&gt; &lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;/p&gt; &lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;]]&gt;" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="vertices" description="">
<NODE name="3" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCCalculator" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-40" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="-400" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" required="true" advanced="false" supported_formats="*.mzML" />
<ITEM name="out" value="" type="output-file" description="Your qcML file." required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="id" value="" type="input-file" description="Input idXML file containing the identifications. Your identifications will be exported in an easy-to-read format" required="false" advanced="false" supported_formats="*.idXML" />
<ITEM name="feature" value="" type="input-file" description="feature input file (this is relevant for most QC issues)" required="false" advanced="false" supported_formats="*.featureXML" />
<ITEM name="consensus" value="" type="input-file" description="consensus input file (this is only used for charge state deconvoluted output. Use the consensusXML output form the DeCharger)" required="false" advanced="false" supported_formats="*.consensusXML" />
<ITEM name="remove_duplicate_features" value="false" type="string" description="This flag should be set, if you work with a set of merged features." required="false" advanced="false" restrictions="true,false" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
<ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="4" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="ImageCreator" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-280" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="-400" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.mzML" />
<ITEM name="in_featureXML" value="" type="input-file" description="input file " required="false" advanced="false" supported_formats="*.featureXML" />
<ITEM name="out" value="" type="output-file" description="output file" required="true" advanced="false" supported_formats="*.png,*.jpg,*.bmp,*.tiff,*.ppm" />
<ITEM name="out_type" value="png" type="string" description="The image format. Set this if you want to force a format not reflected by the &apos;out&apos; filename." required="false" advanced="false" restrictions="png,jpg,bmp,tiff,ppm" />
<ITEM name="width" value="1024" type="int" description="Number of pixels in m/z dimension.#br#If 0, one pixel per Th." required="false" advanced="false" restrictions="0:" />
<ITEM name="height" value="1024" type="int" description="Number of pixels in RT dimension.#br#If 0, one pixel per spectrum." required="false" advanced="false" restrictions="0:" />
<ITEM name="background_color" value="#FFFFFF" type="string" description="Background color e.g.: &quot;#FF0000&quot; to choose red as background color" required="false" advanced="false" />
<ITEM name="feature_color" value="#000000" type="string" description="Feature color e.g.: &quot;#00FF00&quot; to choose green as feature color" required="false" advanced="false" />
<ITEM name="gradient" value="" type="string" description="Intensity gradient that defines colors for the range between 0 and 100.#br#Example: &apos;0,#FFFFFF;50,#FF0000;100,#000000&apos;" required="false" advanced="false" />
<ITEM name="max_intensity" value="0" type="double" description="Maximum peak intensity used to determine range for colors.#br#If 0, this is determined from the data." required="false" advanced="false" />
<ITEM name="log_intensity" value="false" type="string" description="Apply logarithm to intensity values" required="false" advanced="false" restrictions="true,false" />
<ITEM name="transpose" value="true" type="string" description="flag to transpose the resampled matrix (RT vs. m/z).#br#Per default, dimensions run bottom-up in RT and left-right in m/z." required="false" advanced="false" restrictions="true,false" />
<ITEM name="precursors" value="false" type="string" description="Mark locations of MS2 precursors.#br#" required="false" advanced="false" restrictions="true,false" />
<ITEM name="precursor_color" value="#000000" type="string" description="Color for precursor marks (color code or word, e.g. &apos;black&apos;) (requires &apos;precursors&apos; flag to be active)" required="false" advanced="false" />
<ITEM name="precursor_size" value="2" type="int" description="Size of the precursor marks (requires &apos;precursors&apos; flag to be active)" required="false" advanced="false" restrictions="1:3" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
<ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="0" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
<ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
<LISTITEM value="N:/data-NAS/VO/HEK_Lysates_rawfiles/old1.mzML"/>
</ITEMLIST>
<ITEM name="x_pos" value="-280" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="-640" type="double" description="" required="false" advanced="false" />
</NODE>
<NODE name="1" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
<ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
<LISTITEM value="../../Lars/20151026_OpenMS_QC_workflow/QCworkflow_reduced_20151027/old1.featureXML"/>
</ITEMLIST>
<ITEM name="x_pos" value="-40" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="-640" type="double" description="" required="false" advanced="false" />
</NODE>
<NODE name="2" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
<ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
<LISTITEM value="../../Lars/20151026_OpenMS_QC_workflow/QCworkflow_reduced_20151027/old1.idXML"/>
</ITEMLIST>
<ITEM name="x_pos" value="200" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="-640" type="double" description="" required="false" advanced="false" />
</NODE>
<NODE name="5" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCEmbedder" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-40" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="-160" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="Input qcml file" required="false" advanced="false" supported_formats="*.qcML" />
<ITEM name="qp_att_acc" value="QC:0000004" type="string" description="Defines the qp cv accession of the qp to which the table/image is attached." required="false" advanced="false" />
<ITEM name="cv_acc" value="QC:0000055" type="string" description="Defines the cv accession of the attachment." required="true" advanced="false" />
<ITEM name="run" value="" type="input-file" description="The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name." required="false" advanced="false" supported_formats="*.mzML" />
<ITEM name="name" value="" type="string" description="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given." required="false" advanced="false" />
<ITEM name="plot" value="" type="input-file" description="If a plot image is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.PNG" />
<ITEM name="table" value="" type="input-file" description="If a table is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.csv" />
<ITEM name="out" value="" type="output-file" description="Output extended qcML file" required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="6" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCExtractor" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-500" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="400" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="Input qcml file" required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="qp" value="QC:0000038" type="string" description="Target attachment qp." required="true" advanced="false" />
<ITEM name="run" value="" type="input-file" description="The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name." required="false" advanced="false" supported_formats="*.mzML" />
<ITEM name="name" value="" type="string" description="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given." required="false" advanced="false" />
<ITEM name="out_csv" value="" type="output-file" description="Output csv formatted table." required="true" advanced="false" supported_formats="*.csv" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="7" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCExtractor" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-260" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="-20" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="Input qcml file" required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="qp" value="QC:0000044" type="string" description="Target attachment qp." required="true" advanced="false" />
<ITEM name="run" value="" type="input-file" description="The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name." required="false" advanced="false" supported_formats="*.mzML" />
<ITEM name="name" value="" type="string" description="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given." required="false" advanced="false" />
<ITEM name="out_csv" value="" type="output-file" description="Output csv formatted table." required="true" advanced="false" supported_formats="*.csv" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="8" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="Rscript_qcfigures_idmap" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-260" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="140" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="type" value="Rscript_qcfigures_idmap" type="string" description="Which external tool configuration to load?! See &apos;/home/walzer/oms/head/share/OpenMS/TOOLS/EXTERNAL&apos;." required="false" advanced="false" restrictions="hardklor,RAWFileConvert,QCMLExport,RAWDirConvert,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_setid,Rscript_qcfigures_tic,TPP_RefreshParser,mail,TPP_ProteinProphet" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
<NODE name="ETool" description="tool specific parameters">
<ITEM name="scriptpath" value="C:\Program Files\OpenMS-head\share\OpenMS\SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" />
<ITEM name="inTSVprec" value="" type="input-file" description="tabular input data for precursor stats(valid formats: &apos;unknown,tsv&apos;)" required="false" advanced="false" />
<ITEM name="inTSVacc" value="" type="input-file" description="tabular input data for accuracy stats(valid formats: &apos;unknown,tsv&apos;)" required="false" advanced="false" />
<ITEM name="out" value="" type="output-file" description="output figure from R(valid formats: &apos;png&apos;)" required="false" advanced="false" />
</NODE>
</NODE>
</NODE>
<NODE name="9" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCEmbedder" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-40" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="140" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="Input qcml file" required="false" advanced="false" supported_formats="*.qcML" />
<ITEM name="qp_att_acc" value="QC:0000035" type="string" description="Defines the qp cv accession of the qp to which the table/image is attached." required="false" advanced="false" />
<ITEM name="cv_acc" value="QC:0000052" type="string" description="Defines the cv accession of the attachment." required="true" advanced="false" />
<ITEM name="run" value="" type="input-file" description="The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name." required="false" advanced="false" supported_formats="*.mzML" />
<ITEM name="name" value="" type="string" description="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given." required="false" advanced="false" />
<ITEM name="plot" value="" type="input-file" description="If a plot image is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.PNG" />
<ITEM name="table" value="" type="input-file" description="If a table is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.csv" />
<ITEM name="out" value="" type="output-file" description="Output extended qcML file" required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="10" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="Rscript_qcfigures_acc" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-260" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="400" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="type" value="Rscript_qcfigures_acc" type="string" description="Which external tool configuration to load?! See &apos;/home/walzer/oms/head/share/OpenMS/TOOLS/EXTERNAL&apos;." required="false" advanced="false" restrictions="hardklor,RAWFileConvert,QCMLExport,RAWDirConvert,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_setid,Rscript_qcfigures_tic,TPP_RefreshParser,mail,TPP_ProteinProphet" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
<NODE name="ETool" description="tool specific parameters">
<ITEM name="scriptpath" value="C:\Program Files\OpenMS-head\share\OpenMS\SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" />
<ITEM name="inTSVacc" value="" type="input-file" description="tabular input data for accuracy stats(valid formats: &apos;unknown,tsv&apos;)" required="false" advanced="false" />
<ITEM name="out" value="" type="output-file" description="output figure from R(valid formats: &apos;png&apos;)" required="false" advanced="false" />
</NODE>
</NODE>
</NODE>
<NODE name="11" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCEmbedder" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-40" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="400" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="Input qcml file" required="false" advanced="false" supported_formats="*.qcML" />
<ITEM name="qp_att_acc" value="QC:0000041" type="string" description="Defines the qp cv accession of the qp to which the table/image is attached." required="false" advanced="false" />
<ITEM name="cv_acc" value="QC:0000053" type="string" description="Defines the cv accession of the attachment." required="true" advanced="false" />
<ITEM name="run" value="" type="input-file" description="The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name." required="false" advanced="false" supported_formats="*.mzML" />
<ITEM name="name" value="" type="string" description="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given." required="false" advanced="false" />
<ITEM name="plot" value="" type="input-file" description="If a plot image is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.PNG" />
<ITEM name="table" value="" type="input-file" description="If a table is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.csv" />
<ITEM name="out" value="" type="output-file" description="Output extended qcML file" required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="12" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCExtractor" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-500" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="960" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="Input qcml file" required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="qp" value="QC:0000022" type="string" description="Target attachment qp." required="true" advanced="false" />
<ITEM name="run" value="" type="input-file" description="The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name." required="false" advanced="false" supported_formats="*.mzML" />
<ITEM name="name" value="" type="string" description="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given." required="false" advanced="false" />
<ITEM name="out_csv" value="" type="output-file" description="Output csv formatted table." required="true" advanced="false" supported_formats="*.csv" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="13" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="Rscript_qcfigures_tic" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-260" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="960" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="type" value="Rscript_qcfigures_tic" type="string" description="Which external tool configuration to load?! See &apos;/home/walzer/ms-tools/oms-src/share/OpenMS/TOOLS/EXTERNAL&apos;." required="false" advanced="false" restrictions="hardklor,MascotPercolator,RAWFileConvert,MSGFtoPercolator,Percolator,QCMLExport,RAWDirConvert,Rscript_generic,Rscript_mzTab2tsv_PEP,Rscript_mzTab2tsv_PRT,Rscript_mzTab2tsv_PSM,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_setid,Rscript_qcfigures_tic,TPP_RefreshParser,mail,TPP_ProteinProphet" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
<ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
<NODE name="ETool" description="tool specific parameters">
<ITEM name="scriptpath" value="C:\Program Files\OpenMS-head\share\OpenMS\SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" />
<ITEM name="inTSVtic" value="" type="input-file" description="tabular input data for tic stats(valid formats: &apos;unknown,tsv&apos;)" required="false" advanced="false" />
<ITEM name="out" value="" type="output-file" description="output figure from R(valid formats: &apos;png&apos;)" required="false" advanced="false" />
</NODE>
</NODE>
</NODE>
<NODE name="18" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCEmbedder" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-40" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="960" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="Input qcml file" required="false" advanced="false" supported_formats="*.qcML" />
<ITEM name="qp_att_acc" value="QC:0000023" type="string" description="Defines the qp cv accession of the qp to which the table/image is attached." required="false" advanced="false" />
<ITEM name="cv_acc" value="MS:1000235" type="string" description="Defines the cv accession of the attachment." required="true" advanced="false" />
<ITEM name="run" value="" type="input-file" description="The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name." required="false" advanced="false" supported_formats="*.mzML" />
<ITEM name="name" value="" type="string" description="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given." required="false" advanced="false" />
<ITEM name="plot" value="" type="input-file" description="If a plot image is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.PNG" />
<ITEM name="table" value="" type="input-file" description="If a table is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.csv" />
<ITEM name="out" value="" type="output-file" description="Output extended qcML file" required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="20" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-40" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="1460" type="double" description="" required="false" advanced="false" />
<ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="14" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="Rscript_qcfigures_rt_acc" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-260" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="680" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="type" value="Rscript_qcfigures_rt_acc" type="string" description="Which external tool configuration to load?! See &apos;/home/walzer/ms-tools/oms-src/share/OpenMS/TOOLS/EXTERNAL&apos;." required="false" advanced="false" restrictions="hardklor,MascotPercolator,RAWFileConvert,MSGFtoPercolator,Percolator,QCMLExport,RAWDirConvert,Rscript_generic,Rscript_mzTab2tsv_PEP,Rscript_mzTab2tsv_PRT,Rscript_mzTab2tsv_PSM,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_rt_acc,Rscript_qcfigures_setid,Rscript_qcfigures_tic,TPP_RefreshParser,mail,TPP_ProteinProphet" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
<ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
<NODE name="ETool" description="tool specific parameters">
<ITEM name="scriptpath" value="C:\Program Files\OpenMS-head\share\OpenMS\SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" />
<ITEM name="inTSVacc" value="" type="input-file" description="tabular input data for accuracy stats(valid formats: &apos;unknown,tsv&apos;)" required="false" advanced="false" />
<ITEM name="out" value="" type="output-file" description="output figure from R(valid formats: &apos;png&apos;)" required="false" advanced="false" />
</NODE>
</NODE>
</NODE>
<NODE name="15" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCEmbedder" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-40" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="680" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="Input qcml file" required="false" advanced="false" supported_formats="*.qcML" />
<ITEM name="qp_att_acc" value="QC:0000041" type="string" description="Defines the qp cv accession of the qp to which the table/image is attached." required="false" advanced="false" />
<ITEM name="cv_acc" value="QC:0000054" type="string" description="Defines the cv accession of the attachment." required="true" advanced="false" />
<ITEM name="run" value="" type="input-file" description="The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name." required="false" advanced="false" supported_formats="*.mzML" />
<ITEM name="name" value="" type="string" description="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given." required="false" advanced="false" />
<ITEM name="plot" value="" type="input-file" description="If a plot image is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.PNG" />
<ITEM name="table" value="" type="input-file" description="If a table is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.csv" />
<ITEM name="out" value="" type="output-file" description="Output extended qcML file" required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="16" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCExtractor" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-500" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="1220" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="Input qcml file" required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="qp" value="QC:0000018" type="string" description="Target attachment qp." required="true" advanced="false" />
<ITEM name="run" value="" type="input-file" description="The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name." required="false" advanced="false" supported_formats="*.mzML" />
<ITEM name="name" value="" type="string" description="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given." required="false" advanced="false" />
<ITEM name="out_csv" value="" type="output-file" description="Output csv formatted table." required="true" advanced="false" supported_formats="*.csv" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
<NODE name="17" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="Rscript_qcfigures_inj" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-260" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="1220" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="type" value="Rscript_qcfigures_inj" type="string" description="Which external tool configuration to load?! See &apos;/home/walzer/ms-tools/oms-src/share/OpenMS/TOOLS/EXTERNAL&apos;." required="false" advanced="false" restrictions="hardklor,MascotPercolator,RAWFileConvert,MSGFtoPercolator,Percolator,QCMLExport,RAWDirConvert,Rscript_generic,Rscript_mzTab2tsv_PEP,Rscript_mzTab2tsv_PRT,Rscript_mzTab2tsv_PSM,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_rt_acc,Rscript_qcfigures_setid,Rscript_qcfigures_tic,Rscript_qcfigures_inj,TPP_RefreshParser,mail,TPP_ProteinProphet" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
<ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
<NODE name="ETool" description="tool specific parameters">
<ITEM name="scriptpath" value="C:\Program Files\OpenMS-head\share\OpenMS\SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" />
<ITEM name="inTSVfill" value="" type="input-file" description="tabular input data for trap filltimes(valid formats: &apos;unknown,tsv&apos;)" required="false" advanced="false" />
<ITEM name="out" value="" type="output-file" description="output figure from R(valid formats: &apos;png&apos;)" required="false" advanced="false" />
</NODE>
</NODE>
</NODE>
<NODE name="19" description="">
<ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
<ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_name" value="QCEmbedder" type="string" description="" required="false" advanced="false" />
<ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
<ITEM name="x_pos" value="-40" type="double" description="" required="false" advanced="false" />
<ITEM name="y_pos" value="1220" type="double" description="" required="false" advanced="false" />
<NODE name="parameters" description="">
<ITEM name="in" value="" type="input-file" description="Input qcml file" required="false" advanced="false" supported_formats="*.qcML" />
<ITEM name="qp_att_acc" value="QC:0000023" type="string" description="Defines the qp cv accession of the qp to which the table/image is attached." required="false" advanced="false" />
<ITEM name="cv_acc" value="QC:0000051" type="string" description="Defines the cv accession of the attachment." required="true" advanced="false" />
<ITEM name="run" value="" type="input-file" description="The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name." required="false" advanced="false" supported_formats="*.mzML" />
<ITEM name="name" value="" type="string" description="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given." required="false" advanced="false" />
<ITEM name="plot" value="" type="input-file" description="If a plot image is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.PNG" />
<ITEM name="table" value="" type="input-file" description="If a table is to be attached to a qp, this has to be specified here." required="false" advanced="false" supported_formats="*.csv" />
<ITEM name="out" value="" type="output-file" description="Output extended qcML file" required="true" advanced="false" supported_formats="*.qcML" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
</NODE>
</NODE>
</NODE>
<NODE name="edges" description="">
<NODE name="0" description="">
<NODE name="source/target" description="">
<ITEM name="" value="0/3" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="source_out_param" description="">
<ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="target_in_param" description="">
<ITEM name="" value="in" type="string" description="" required="false" advanced="false" />
</NODE>
</NODE>
<NODE name="1" description="">
<NODE name="source/target" description="">
<ITEM name="" value="0/4" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="source_out_param" description="">
<ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="target_in_param" description="">
<ITEM name="" value="in" type="string" description="" required="false" advanced="false" />
</NODE>
</NODE>
<NODE name="2" description="">
<NODE name="source/target" description="">
<ITEM name="" value="1/3" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="source_out_param" description="">
<ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="target_in_param" description="">
<ITEM name="" value="feature" type="string" description="" required="false" advanced="false" />
</NODE>
</NODE>
<NODE name="3" description="">
<NODE name="source/target" description="">
<ITEM name="" value="2/3" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="source_out_param" description="">
<ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="target_in_param" description="">
<ITEM name="" value="id" type="string" description="" required="false" advanced="false" />
</NODE>
</NODE>
<NODE name="4" description="">
<NODE name="source/target" description="">
<ITEM name="" value="3/5" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="source_out_param" description="">
<ITEM name="" value="out" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="target_in_param" description="">
<ITEM name="" value="in" type="string" description="" required="false" advanced="false" />
</NODE>
</NODE>
<NODE name="5" description="">
<NODE name="source/target" description="">
<ITEM name="" value="4/5" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="source_out_param" description="">
<ITEM name="" value="out" type="string" description="" required="false" advanced="false" />
</NODE>
<NODE name="target_in_param" description="">
<ITEM name="" value="plot" type="string" description="" required="false" advanced="false" />
</NODE>
</NODE>
<NODE name="6" description="">
<NODE name="source/target" description="">
<ITEM name="" value="8/9" type="string" description="" required="false" advanced="false" />
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<ITEM name="" value="ETool:out" type="string" description="" required="false" advanced="false" />
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<ITEM name="" value="ETool:inTSVacc" type="string" description="" required="false" advanced="false" />
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<ITEM name="" value="plot" type="string" description="" required="false" advanced="false" />
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<ITEM name="" value="in" type="string" description="" required="false" advanced="false" />
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<ITEM name="" value="out_csv" type="string" description="" required="false" advanced="false" />
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<ITEM name="" value="ETool:out" type="string" description="" required="false" advanced="false" />
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<ITEM name="" value="plot" type="string" description="" required="false" advanced="false" />
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<ITEM name="" value="out" type="string" description="" required="false" advanced="false" />
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<ITEM name="" value="out" type="string" description="" required="false" advanced="false" />
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<NODE name="target_in_param" description="">
<ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" />
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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