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1 <tool id="openms_id_filter" version="0.1.0" name="ID Filter">
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2 <description>
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3 Filters protein identification engine results by different criteria.
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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 'IDFilter' --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=$output
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17 score!pep=$peptide_score
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18 score!prot=$protein_score
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19 thresh!pep=$peptide_threshold
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20 thresh!prot=$protein_threshold
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21 best!n_peptide_hits=$n_peptide_hits
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22 best!n_protein_hits=$n_protein_hits
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23 </configfile>
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24 </configfiles>
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25 <inputs>
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26 <param name="input1" label="Input" type="data" format="idxml" />
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27 <param name="n_peptide_hits" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n>0). " value="0" type="integer" />
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28 <param name="n_protein_hits" label="Keep only the 'n' highest scoring protein hits per spectrum (for n>0). " value="0" type="integer" />
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29 <param name="peptide_score" label="Peptide Score. " value="0" type="float" help="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc. (default: '0')" />
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30 <param name="protein_score" label="Protein Score. " value="0" type="float" help="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc. (default: '0')" />
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31 <param name="peptide_threshold" label="Peptide Threshold" help="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." value="0" type="float" />
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32 <param name="protein_threshold" label="Protein Threshold" help="Keep a protein hit only if its score is above this fraction of the peptide significance threshold." value="0" type="float" />
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33 </inputs>
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34 <outputs>
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35 <data format="idxml" name="output" />
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36 </outputs>
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37 <help>
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38 **What it does**
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39
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40 This tool is used to filter the identifications found by a peptide/protein identification tool like Mascot. Different filters can be applied.
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41
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42 **Citation**
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43
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44 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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45
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46 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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47 </help>
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48 </tool>
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