Mercurial > repos > galaxyp > openms
comparison id_filter.xml @ 2:cf0d72c7b482 draft
Update.
| author | galaxyp |
|---|---|
| date | Fri, 10 May 2013 17:31:05 -0400 |
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| 1:5c65f8116244 | 2:cf0d72c7b482 |
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| 1 <tool id="openms_id_filter" version="0.1.0" name="ID Filter"> | |
| 2 <description> | |
| 3 Filters protein identification engine results by different criteria. | |
| 4 </description> | |
| 5 <macros> | |
| 6 <import>macros.xml</import> | |
| 7 </macros> | |
| 8 <expand macro="stdio" /> | |
| 9 <expand macro="requires" /> | |
| 10 <command interpreter="python"> | |
| 11 openms_wrapper.py --executable 'IDFilter' --config $config | |
| 12 </command> | |
| 13 <configfiles> | |
| 14 <configfile name="config">[simple_options] | |
| 15 in=$input1 | |
| 16 out=$output | |
| 17 score!pep=$peptide_score | |
| 18 score!prot=$protein_score | |
| 19 thresh!pep=$peptide_threshold | |
| 20 thresh!prot=$protein_threshold | |
| 21 best!n_peptide_hits=$n_peptide_hits | |
| 22 best!n_protein_hits=$n_protein_hits | |
| 23 </configfile> | |
| 24 </configfiles> | |
| 25 <inputs> | |
| 26 <param name="input1" label="Input" type="data" format="idxml" /> | |
| 27 <param name="n_peptide_hits" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n>0). " value="0" type="integer" /> | |
| 28 <param name="n_protein_hits" label="Keep only the 'n' highest scoring protein hits per spectrum (for n>0). " value="0" type="integer" /> | |
| 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')" /> | |
| 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')" /> | |
| 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" /> | |
| 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" /> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data format="idxml" name="output" /> | |
| 36 </outputs> | |
| 37 <help> | |
| 38 **What it does** | |
| 39 | |
| 40 This tool is used to filter the identifications found by a peptide/protein identification tool like Mascot. Different filters can be applied. | |
| 41 | |
| 42 **Citation** | |
| 43 | |
| 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.`` | |
| 45 | |
| 46 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms | |
| 47 </help> | |
| 48 </tool> |