- old website's workflow -

SILACquantitationOrbiXL_TPPidentification_old.toppas

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  <NODE name="info" description="">
    <ITEM name="version" value="1.9.0" type="string" description="" />
    <ITEM name="num_vertices" value="9" type="int" description="" />
    <ITEM name="num_edges" value="8" type="int" description="" />
    <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;
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&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;
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&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;SILAC analysis pipeline for Thermo Orbi XL data with identification from TPP&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;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;input [1]: mzML&lt;/p&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;input [3]: pepXML from TPP&lt;/p&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;input [4]: protXML from TPP&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;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;output [9]: protein abundances&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;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;SILAC peptide pairs are detected in [2]. Protein group information in [4] will be incorporated in the final result.&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;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Lars Nilse l.nilse@dunelm.org.uk&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;
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  <NODE name="vertices" description="">
    <NODE name="0" description="">
      <ITEM name="recycle_output" value="false" type="string" description="" />
      <ITEM name="toppas_type" value="input file list" type="string" description="" />
      <ITEMLIST name="file_names" type="string" description="">
        <LISTITEM value="20120327_benchmark/yeast/Bert_20080625_BJS_yeast_1-1_01.mzML"/>
      </ITEMLIST>
      <ITEM name="x_pos" value="280" type="float" description="" />
      <ITEM name="y_pos" value="-820" type="float" description="" />
    </NODE>
    <NODE name="8" description="">
      <ITEM name="recycle_output" value="false" type="string" description="" />
      <ITEM name="toppas_type" value="output file list" type="string" description="" />
      <ITEM name="x_pos" value="520" type="float" description="" />
      <ITEM name="y_pos" value="0" type="float" description="" />
    </NODE>
    <NODE name="1" description="">
      <ITEM name="recycle_output" value="false" type="string" description="" />
      <ITEM name="toppas_type" value="tool" type="string" description="" />
      <ITEM name="tool_name" value="SILACAnalyzer" type="string" description="" />
      <ITEM name="tool_type" value="" type="string" description="" />
      <ITEM name="x_pos" value="280" type="float" description="" />
      <ITEM name="y_pos" value="-640" type="float" description="" />
      <NODE name="parameters" description="">
        <ITEM name="in" value="" type="string" description="Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided data!)" tags="input file,required" restrictions="*.mzML" />
        <ITEM name="out" value="" type="string" description="Set of all identified peptide groups (i.e. peptide pairs or triplets or singlets or ..). The m/z-RT positions correspond to the lightest peptide in each group." tags="output file" restrictions="*.consensusXML" />
        <ITEM name="out_clusters" value="" type="string" description="Optional debug output containing data points passing all filters, hence belonging to a SILAC pattern. Points of the same colour correspond to the mono-isotopic peak of the lightest peptide in a pattern." tags="advanced,output file" restrictions="*.consensusXML" />
        <ITEM name="out_features" value="" type="string" description="Optional output file containing the individual peptide features in &apos;out&apos;." tags="advanced,output file" restrictions="*.featureXML" />
        <ITEM name="out_filters" value="" type="string" description="Optional output file containing all points that passed the filters as txt. Suitable as input for &apos;in_filters&apos; to perform clustering without preceding filtering process." tags="advanced,output file" restrictions="*.consensusXML" />
        <ITEM name="in_filters" value="" type="string" description="Optional input file containing all points that passed the filters as txt. Use output from &apos;out_filters&apos; to perform clustering only." tags="advanced,output file" restrictions="*.consensusXML" />
        <ITEM name="out_debug" value="" type="string" description="Filename base for debug output." tags="advanced" />
        <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
        <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
        <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
        <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
        <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
        <NODE name="algorithm" description="Parameters for the algorithm.">
          <ITEM name="allow_missing_peaks" value="true" type="string" description="Low intensity peaks might be missing from the isotopic pattern of some of the peptides. Should such peptides be included in the analysis?" tags="advanced" restrictions="true,false" />
          <ITEM name="rt_threshold" value="30" type="float" description="Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)" restrictions="0:" />
          <ITEM name="rt_min" value="1" type="float" description="Lower bound for the retention time [s]." restrictions="0:" />
          <ITEM name="intensity_cutoff" value="10000" type="float" description="Lower bound for the intensity of isotopic peaks in a SILAC pattern." restrictions="0:" />
          <ITEM name="intensity_correlation" value="0.6" type="float" description="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." restrictions="0:1" />
          <ITEM name="model_deviation" value="5" type="float" description="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) &lt; observed_ratio &lt; ( theoretic_ratio * model_deviation )." restrictions="1:" />
        </NODE>
        <NODE name="labels" description="Isotopic labels that can be specified in section &apos;sample&apos;.">
          <ITEM name="Arg6" value="6.0201290268" type="float" description="Arg6 mass shift" tags="advanced" restrictions="0:" />
          <ITEM name="Arg10" value="10.0082686" type="float" description="Arg10 mass shift" tags="advanced" restrictions="0:" />
          <ITEM name="Lys4" value="4.0251069836" type="float" description="Lys4 mass shift" tags="advanced" restrictions="0:" />
          <ITEM name="Lys6" value="6.0201290268" type="float" description="Lys6 mass shift" tags="advanced" restrictions="0:" />
          <ITEM name="Lys8" value="8.0141988132" type="float" description="Lys8 mass shift" tags="advanced" restrictions="0:" />
          <ITEM name="dICPL4" value="4.025107" type="float" description="mass difference between isotope-coded protein labels ICPL 4 and ICPL 0" tags="advanced" restrictions="0:" />
          <ITEM name="dICPL6" value="6.020129" type="float" description="mass difference between isotope-coded protein labels ICPL 6 and ICPL 0" tags="advanced" restrictions="0:" />
          <ITEM name="dICPL10" value="10.045236" type="float" description="mass difference between isotope-coded protein labels ICPL 10 and ICPL 0" tags="advanced" restrictions="0:" />
          <ITEM name="Methyl4" value="4.0202" type="float" description="Methyl4 mass shift" tags="advanced" restrictions="0:" />
          <ITEM name="Methyl8" value="8.0202" type="float" description="Methyl8 mass shift" tags="advanced" restrictions="0:" />
          <ITEM name="Methyl12" value="12.0202" type="float" description="Methyl12 mass shift" tags="advanced" restrictions="0:" />
          <ITEM name="Methyl16" value="16.0202" type="float" description="Methyl16 mass shift" tags="advanced" restrictions="0:" />
          <ITEM name="Methyl24" value="24.0202" type="float" description="Methyl24 mass shift" tags="advanced" restrictions="0:" />
          <ITEM name="Methyl32" value="32.0202" type="float" description="Methyl32 mass shift" tags="advanced" restrictions="0:" />
        </NODE>
        <NODE name="sample" description="Parameters describing the sample and its labels.">
          <ITEM name="labels" value="[Lys8,Arg10]" type="string" description="Labels used for labelling the sample. [...] specifies the labels for a single sample. For example, [Lys4,Arg6][Lys8,Arg10] describes a mixtures of three samples. One of them unlabelled, one labelled with Lys4 and Arg6 and a third one with Lys8 and Arg10. For permitted labels see &apos;advanced parameters&apos;, section &apos;labels&apos;. If left empty the tool identifies singlets, i.e. acts as peptide feature finder." />
          <ITEM name="charge" value="1:5" type="string" description="Range of charge states in the sample, i.e. min charge : max charge." />
          <ITEM name="missed_cleavages" value="2" type="int" description="Maximum number of missed cleavages." restrictions="0:" />
          <ITEM name="peaks_per_peptide" value="3:6" type="string" description="Range of peaks per peptide in the sample, i.e. min peaks per peptide : max peaks per peptide. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " tags="advanced" />
        </NODE>
      </NODE>
    </NODE>
    <NODE name="6" description="">
      <ITEM name="recycle_output" value="false" type="string" description="" />
      <ITEM name="toppas_type" value="tool" type="string" description="" />
      <ITEM name="tool_name" value="IDMapper" type="string" description="" />
      <ITEM name="tool_type" value="" type="string" description="" />
      <ITEM name="x_pos" value="520" type="float" description="" />
      <ITEM name="y_pos" value="-420" type="float" description="" />
      <NODE name="parameters" description="">
        <ITEM name="id" value="" type="string" description="Protein/peptide identifications file" tags="input file,required" restrictions="*.idXML" />
        <ITEM name="in" value="" type="string" description="Feature map/consensus map file" tags="input file,required" restrictions="*.featureXML,*.consensusXML" />
        <ITEM name="out" value="" type="string" description="Output file (the format depends on the input file format)." tags="output file,required" restrictions="*.featureXML,*.consensusXML" />
        <ITEM name="rt_tolerance" value="20" type="float" description="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as &apos;plus or minus x&apos;, so the matching range increases by twice the given value." restrictions="0:" />
        <ITEM name="mz_tolerance" value="10" type="float" description="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as &apos;plus or minus x&apos;, so the matching range increases by twice the given value." restrictions="0:" />
        <ITEM name="mz_measure" value="ppm" type="string" description="Unit of &apos;mz_tolerance&apos;." restrictions="ppm,Da" />
        <ITEM name="mz_reference" value="precursor" type="string" description="Source of m/z values for peptide identifications. If &apos;precursor&apos;, the precursor-m/z from the idXML is used. If &apos;peptide&apos;,#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#(&apos;peptide&apos; should be used together with &apos;use_centroid_mz&apos; to avoid false-positive matches.)" restrictions="precursor,peptide" />
        <ITEM name="ignore_charge" value="false" type="string" description="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." restrictions="true,false" />
        <ITEM name="use_centroid_rt" value="false" type="string" description="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." restrictions="true,false" />
        <ITEM name="use_centroid_mz" value="false" type="string" description="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.#br#(If you choose &apos;peptide&apos; as &apos;mz_reference&apos;, you should usually set this flag to avoid false-positive matches.)" restrictions="true,false" />
        <ITEM name="use_subelements" value="true" type="string" description="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." restrictions="true,false" />
        <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
        <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
        <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
        <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
        <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
      </NODE>
    </NODE>
    <NODE name="7" description="">
      <ITEM name="recycle_output" value="false" type="string" description="" />
      <ITEM name="toppas_type" value="tool" type="string" description="" />
      <ITEM name="tool_name" value="ProteinQuantifier" type="string" description="" />
      <ITEM name="tool_type" value="" type="string" description="" />
      <ITEM name="x_pos" value="520" type="float" description="" />
      <ITEM name="y_pos" value="-200" type="float" description="" />
      <NODE name="parameters" description="">
        <ITEM name="in" value="" type="string" description="Input file" tags="input file,required" restrictions="*.featureXML,*.consensusXML" />
        <ITEM name="protxml" value="" type="string" description="ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.#br#Information about indistinguishable proteins will be used for protein quantification." tags="input file" restrictions="*.idXML" />
        <ITEM name="out" value="" type="string" description="Output file for protein abundances" tags="output file" />
        <ITEM name="peptide_out" value="" type="string" description="Output file for peptide abundances" tags="output file" />
        <ITEM name="id_out" value="" type="string" description="Output file for peptide and protein abundances (annotated idXML) - suitable for export to mzTab.#br#Either &apos;out&apos;, &apos;peptide_out&apos;, or &apos;id_out&apos; are required. They can be used together." tags="output file" restrictions="*.idXML" />
        <ITEM name="top" value="1" type="int" description="Calculate protein abundance from this number of proteotypic peptides (most abundant first; &apos;0&apos; for all)" restrictions="0:" />
        <ITEM name="average" value="median" type="string" description="Averaging method used to compute protein abundances from peptide abundances" restrictions="median,mean,sum" />
        <ITEM name="include_all" value="false" type="string" description="Include results for proteins with fewer proteotypic peptides than indicated by &apos;top&apos; (no effect if &apos;top&apos; is 0 or 1)" restrictions="true,false" />
        <ITEM name="filter_charge" value="false" type="string" description="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." restrictions="true,false" />
        <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
        <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
        <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
        <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
        <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
        <NODE name="consensus" description="Additional options for consensus maps">
          <ITEM name="normalize" value="false" type="string" description="Scale peptide abundances so that medians of all samples are equal" restrictions="true,false" />
          <ITEM name="fix_peptides" value="false" type="string" description="Use the same peptides for protein quantification across all samples.#br#With &apos;top 0&apos;, all peptides that occur in every sample are considered.#br#Otherwise (&apos;top N&apos;), the N peptides that occur in the most samples (independently of each other) are selected,#br#breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)." restrictions="true,false" />
        </NODE>
        <NODE name="format" description="Output formatting options">
          <ITEM name="separator" value="," type="string" description="Character(s) used to separate fields; by default, the &apos;tab&apos; character is used" />
          <ITEM name="quoting" value="double" type="string" description="Method for quoting of strings: &apos;none&apos; for no quoting, &apos;double&apos; for quoting with doubling of embedded quotes,#br#&apos;escape&apos; for quoting with backslash-escaping of embedded quotes" restrictions="none,double,escape" />
          <ITEM name="replacement" value="_" type="string" description="If &apos;quoting&apos; is &apos;none&apos;, used to replace occurrences of the separator in strings before writing" />
        </NODE>
      </NODE>
    </NODE>
    <NODE name="2" description="">
      <ITEM name="recycle_output" value="false" type="string" description="" />
      <ITEM name="toppas_type" value="input file list" type="string" description="" />
      <ITEMLIST name="file_names" type="string" description="">
      </ITEMLIST>
      <ITEM name="x_pos" value="520" type="float" description="" />
      <ITEM name="y_pos" value="-820" type="float" description="" />
    </NODE>
    <NODE name="3" description="">
      <ITEM name="recycle_output" value="false" type="string" description="" />
      <ITEM name="toppas_type" value="input file list" type="string" description="" />
      <ITEMLIST name="file_names" type="string" description="">
      </ITEMLIST>
      <ITEM name="x_pos" value="780" type="float" description="" />
      <ITEM name="y_pos" value="-820" type="float" description="" />
    </NODE>
    <NODE name="4" description="">
      <ITEM name="recycle_output" value="false" type="string" description="" />
      <ITEM name="toppas_type" value="tool" type="string" description="" />
      <ITEM name="tool_name" value="IDFileConverter" type="string" description="" />
      <ITEM name="tool_type" value="" type="string" description="" />
      <ITEM name="x_pos" value="520" type="float" description="" />
      <ITEM name="y_pos" value="-640" type="float" description="" />
      <NODE name="parameters" description="">
        <ITEM name="in" value="" type="string" description="Input file or directory containing the output of the search engine.#br#Sequest: Directory containing the .out files#br#pepXML: Single pepXML file.#br#protXML: Single protXML file.#br#xml: Single mascot XML file.#br#idXML: Single idXML file.#br#" tags="input file,required" />
        <ITEM name="out" value="" type="string" description="Output file" tags="output file,required" restrictions="*.idXML,*.mzid,*.pepXML,*.FASTA" />
        <ITEM name="out_type" value="idXML" type="string" description="output file type -- default: determined from file extension or content#br#" restrictions="idXML,mzid,pepXML,FASTA" />
        <ITEM name="mz_file" value="" type="string" description="MS data file from which the pepXML was generated. Used to look up retention times (some pepXMLs contain only scan numbers) and/or to define what parts to extract (some pepXMLs contain results from multiple experiments)." />
        <ITEM name="ignore_proteins_per_peptide" value="false" type="string" description="Workaround to deal with .out files that contain e.g. &quot;+1&quot; in references column,#br#but do not list extra references in subsequent lines (try -debug 3 or 4)" tags="advanced" restrictions="true,false" />
        <ITEM name="mz_name" value="" type="string" description="Experiment filename/path to match in the pepXML file (&apos;base_name&apos; attribute). Only necessary if different from &apos;mz_file&apos;." />
        <ITEM name="use_precursor_data" value="false" type="string" description="Use precursor RTs (and m/z values) from &apos;mz_file&apos; for the generated peptide identifications, instead of the RTs of MS2 spectra." restrictions="true,false" />
        <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
        <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
        <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
        <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
        <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
      </NODE>
    </NODE>
    <NODE name="5" description="">
      <ITEM name="recycle_output" value="false" type="string" description="" />
      <ITEM name="toppas_type" value="tool" type="string" description="" />
      <ITEM name="tool_name" value="IDFileConverter" type="string" description="" />
      <ITEM name="tool_type" value="" type="string" description="" />
      <ITEM name="x_pos" value="780" type="float" description="" />
      <ITEM name="y_pos" value="-640" type="float" description="" />
      <NODE name="parameters" description="">
        <ITEM name="in" value="" type="string" description="Input file or directory containing the output of the search engine.#br#Sequest: Directory containing the .out files#br#pepXML: Single pepXML file.#br#protXML: Single protXML file.#br#xml: Single mascot XML file.#br#idXML: Single idXML file.#br#" tags="input file,required" />
        <ITEM name="out" value="" type="string" description="Output file" tags="output file,required" restrictions="*.idXML,*.mzid,*.pepXML,*.FASTA" />
        <ITEM name="out_type" value="idXML" type="string" description="output file type -- default: determined from file extension or content#br#" restrictions="idXML,mzid,pepXML,FASTA" />
        <ITEM name="mz_file" value="" type="string" description="MS data file from which the pepXML was generated. Used to look up retention times (some pepXMLs contain only scan numbers) and/or to define what parts to extract (some pepXMLs contain results from multiple experiments)." />
        <ITEM name="ignore_proteins_per_peptide" value="false" type="string" description="Workaround to deal with .out files that contain e.g. &quot;+1&quot; in references column,#br#but do not list extra references in subsequent lines (try -debug 3 or 4)" tags="advanced" restrictions="true,false" />
        <ITEM name="mz_name" value="" type="string" description="Experiment filename/path to match in the pepXML file (&apos;base_name&apos; attribute). Only necessary if different from &apos;mz_file&apos;." />
        <ITEM name="use_precursor_data" value="false" type="string" description="Use precursor RTs (and m/z values) from &apos;mz_file&apos; for the generated peptide identifications, instead of the RTs of MS2 spectra." restrictions="true,false" />
        <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
        <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
        <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
        <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
        <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
      </NODE>
    </NODE>
  </NODE>
  <NODE name="edges" description="">
    <NODE name="0" description="">
      <NODE name="source/target" description="">
        <ITEM name="" value="1/6" type="string" description="" />
      </NODE>
      <NODE name="source_out_param" description="">
        <ITEM name="" value="out" type="string" description="" />
      </NODE>
      <NODE name="target_in_param" description="">
        <ITEM name="" value="in" type="string" description="" />
      </NODE>
    </NODE>
    <NODE name="1" description="">
      <NODE name="source/target" description="">
        <ITEM name="" value="0/1" type="string" description="" />
      </NODE>
      <NODE name="source_out_param" description="">
        <ITEM name="" value="__no_name__" type="string" description="" />
      </NODE>
      <NODE name="target_in_param" description="">
        <ITEM name="" value="in" type="string" description="" />
      </NODE>
    </NODE>
    <NODE name="2" description="">
      <NODE name="source/target" description="">
        <ITEM name="" value="7/8" type="string" description="" />
      </NODE>
      <NODE name="source_out_param" description="">
        <ITEM name="" value="out" type="string" description="" />
      </NODE>
      <NODE name="target_in_param" description="">
        <ITEM name="" value="__no_name__" type="string" description="" />
      </NODE>
    </NODE>
    <NODE name="3" description="">
      <NODE name="source/target" description="">
        <ITEM name="" value="6/7" type="string" description="" />
      </NODE>
      <NODE name="source_out_param" description="">
        <ITEM name="" value="out" type="string" description="" />
      </NODE>
      <NODE name="target_in_param" description="">
        <ITEM name="" value="in" type="string" description="" />
      </NODE>
    </NODE>
    <NODE name="4" description="">
      <NODE name="source/target" description="">
        <ITEM name="" value="2/4" type="string" description="" />
      </NODE>
      <NODE name="source_out_param" description="">
        <ITEM name="" value="__no_name__" type="string" description="" />
      </NODE>
      <NODE name="target_in_param" description="">
        <ITEM name="" value="in" type="string" description="" />
      </NODE>
    </NODE>
    <NODE name="5" description="">
      <NODE name="source/target" description="">
        <ITEM name="" value="3/5" type="string" description="" />
      </NODE>
      <NODE name="source_out_param" description="">
        <ITEM name="" value="__no_name__" type="string" description="" />
      </NODE>
      <NODE name="target_in_param" description="">
        <ITEM name="" value="in" type="string" description="" />
      </NODE>
    </NODE>
    <NODE name="6" description="">
      <NODE name="source/target" description="">
        <ITEM name="" value="4/6" type="string" description="" />
      </NODE>
      <NODE name="source_out_param" description="">
        <ITEM name="" value="out" type="string" description="" />
      </NODE>
      <NODE name="target_in_param" description="">
        <ITEM name="" value="id" type="string" description="" />
      </NODE>
    </NODE>
    <NODE name="7" description="">
      <NODE name="source/target" description="">
        <ITEM name="" value="5/7" type="string" description="" />
      </NODE>
      <NODE name="source_out_param" description="">
        <ITEM name="" value="out" type="string" description="" />
      </NODE>
      <NODE name="target_in_param" description="">
        <ITEM name="" value="protxml" type="string" description="" />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>

from old website's workflow section:

SILAC analysis pipeline for Thermo Orbi XL data with identification from TPP

input [1]: mzML
input [3]: pepXML from TPP
input [4]: protXML from TPP

output [9]: protein abundances

SILAC peptide pairs are detected in [2]. Protein group information in [4] will be incorporated in the final result.

Lars Nilse l.nilse@dunelm.org.uk