Mercurial > repos > galaxyp > openms
comparison protein_inference.xml @ 2:cf0d72c7b482 draft
Update.
| author | galaxyp |
|---|---|
| date | Fri, 10 May 2013 17:31:05 -0400 |
| parents | |
| children | 1183846e70a1 |
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| 1:5c65f8116244 | 2:cf0d72c7b482 |
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| 1 <tool id="openms_protein_inference" version="0.1.0" name="Protein Inference"> | |
| 2 <description> | |
| 3 Computes a protein identification based on the number of identified peptides. | |
| 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 'PeptideIndexer' --config $config | |
| 12 </command> | |
| 13 <configfiles> | |
| 14 <configfile name="config">[simple_options] | |
| 15 in=$input1 | |
| 16 out=$output | |
| 17 min_peptides_per_protein=${min_peptides_per_protein} | |
| 18 treat_charge_variants_separately=${treat_charge_variants_separately} | |
| 19 treat_modification_variants_separately=${treat_modification_variants_separately} | |
| 20 </configfile> | |
| 21 </configfiles> | |
| 22 <inputs> | |
| 23 <param name="input1" label="Identification Input" type="data" format="idxml" /> | |
| 24 <param name="min_peptides_per_protein" type="integer" value="2" label="Minimum Number of Peptides per Protein Identification" /> | |
| 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." /> | |
| 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." /> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data format="idxml" name="output" /> | |
| 30 </outputs> | |
| 31 <help> | |
| 32 **What it does** | |
| 33 | |
| 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. | |
| 35 | |
| 36 **Citation** | |
| 37 | |
| 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.`` | |
| 39 | |
| 40 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms | |
| 41 </help> | |
| 42 </tool> |