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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="IDMerger" name="IDMerger" version="1.12.0">
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3 <description>Merges several protein/peptide identification files into one file.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">IDMerger</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>IDMerger
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -add_to ${param_add_to}
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15 ${param_annotate_file_origin}
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16 ${param_pepxml_protxml}
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17 -threads \${GALAXY_SLOTS:-24}
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18 </command>
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19 <inputs>
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20 <param name="param_in" type="data" format="idXML" optional="False" size="20" label="Input files separated by blanks" help="(-in)"/>
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21 <param name="param_add_to" type="data" format="idXML" optional="True" label="Optional input file. IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)." help="(-add_to)"/>
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22 <param name="param_annotate_file_origin" type="boolean" truevalue="-annotate_file_origin true" falsevalue="-annotate_file_origin false" checked="false" optional="True" label="Store the original filename in each protein/peptide identification (meta value: file_origin)." help="(-annotate_file_origin)"/>
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23 <param name="param_pepxml_protxml" type="boolean" truevalue="-pepxml_protxml true" falsevalue="-pepxml_protxml false" checked="false" optional="True" label="Merge idXML files derived from a pepXML and corresponding protXML file.#br#Exactly two input files are expected in this case. Not compatible with 'add_to'." help="(-pepxml_protxml)"/>
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24 </inputs>
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25 <outputs>
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26 <data name="param_out" label="Output file" format="idXML"/>
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27 </outputs>
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28 <help>**What it does**
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29
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30 Merges several protein/peptide identification files into one file.
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31
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32
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33 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html
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34
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35 @REFERENCES@
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36 </help>
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37 </tool>
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