Created
September 26, 2015 10:06
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OpenMS workflow, appends shuffled decoy database, 26/09/2015
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| <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=""> | |
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| <ITEM name="num_vertices" value="3" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="2" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> | |
| <html><head><meta name="qrichtext" content="1" /><style type="text/css"> | |
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| <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Appends a shuffled version to the target input fasta database. Decoy proteins are denoted by a prefix &quot;dec_&quot;.</p></body></html>]]>" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="vertices" description=""> | |
| <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="../../proteome-databases/uniprot-human-Nov26-2013-reference-reviewed-canonical-without-isoforms.fasta"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-1040" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-1020" 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="output file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-1040" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-660" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> | |
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| <NODE name="1" 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="DecoyDatabase" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-1040" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-840" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEMLIST name="in" type="input-file" description="Input FASTA file(s), each containing a database. It is recommended to include a contaminant database as well." required="true" advanced="false" supported_formats="*.fasta"> | |
| </ITEMLIST> | |
| <ITEM name="out" value="" type="output-file" description="Output FASTA file where the decoy database will be written to." required="true" advanced="false" supported_formats="*.fasta" /> | |
| <ITEM name="decoy_string" value="dec_" type="string" description="String that is appended to the accession of the protein database to indicate a decoy protein." required="false" advanced="false" /> | |
| <ITEM name="decoy_string_position" value="prefix" type="string" description="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" required="false" advanced="false" restrictions="prefix,suffix" /> | |
| <ITEM name="append" value="true" type="string" description="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="shuffle" value="true" type="string" description="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" 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="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="0/1" 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" /> | |
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| </NODE> | |
| <NODE name="1" description=""> | |
| <NODE name="source/target" description=""> | |
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| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
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| </PARAMETERS> |
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