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1 <tool id="openms_protein_inference" version="0.1.0" name="Protein Inference">
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2 <description>
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3 Computes a protein identification based on the number of identified peptides.
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4 </description>
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5 <macros>
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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="requires" />
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10 <command interpreter="python">
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11 openms_wrapper.py --executable 'PeptideIndexer' --config $config
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12 </command>
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13 <configfiles>
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14 <configfile name="config">[simple_options]
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15 in=$input1
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16 out=$output
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17 min_peptides_per_protein=${min_peptides_per_protein}
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18 treat_charge_variants_separately=${treat_charge_variants_separately}
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19 treat_modification_variants_separately=${treat_modification_variants_separately}
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20 </configfile>
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21 </configfiles>
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22 <inputs>
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23 <param name="input1" label="Identification Input" type="data" format="idxml" />
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24 <param name="min_peptides_per_protein" type="integer" value="2" label="Minimum Number of Peptides per Protein Identification" />
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25 <param name="treat_charge_variants_separately" label="Treat Charge Variants Separately" type="boolean" truevalue="true" falsevalue="false" checked="false" help="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences." />
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26 <param name="treat_modification_variants_separately" label="Treat Modification Variants Separately" type="boolean" truevalue="true" falsevalue="false" checked="false" help="If this flag is set, different modification variants of the same peptide sequence count as individual evidences." />
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27 </inputs>
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28 <outputs>
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29 <data format="idxml" name="output" />
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30 </outputs>
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31 <help>
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32 **What it does**
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33
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34 This tool counts the peptide sequences that match a protein accession. From this count for all protein hits in the respective id run, only those proteins are accepted that have at least a given number of peptides sequences identified. The peptide identifications should be prefiltered with respect to false discovery rate and the score in general to remove bad identifications.
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35
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36 **Citation**
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37
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38 For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
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39
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40 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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41 </help>
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42 </tool>
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