Mercurial > repos > iracooke > tpp_prophets
comparison interprophet.xml @ 0:adf8ac7aa6c8
Uploaded
| author | iracooke |
|---|---|
| date | Thu, 06 Jun 2013 01:33:00 -0400 |
| parents | |
| children | a9f016a531a5 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:adf8ac7aa6c8 |
|---|---|
| 1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1"> | |
| 2 | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.2.0">galaxy_protk</requirement> | |
| 5 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> | |
| 6 </requirements> | |
| 7 | |
| 8 | |
| 9 <description>Combine Peptide Prophet results from multiple search engines</description> | |
| 10 | |
| 11 <command interpreter="ruby"> | |
| 12 | |
| 13 interprophet_wrapper.rb $output $use_nss $use_nrs $use_nse $use_nsi $use_nsm --minprob $minprob | |
| 14 | |
| 15 | |
| 16 ## Inputs. | |
| 17 ${first_input} | |
| 18 #for $input_file in $input_files: | |
| 19 ${input_file.additional_input} | |
| 20 #end for | |
| 21 | |
| 22 </command> | |
| 23 | |
| 24 <inputs> | |
| 25 | |
| 26 <param name="first_input" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> | |
| 27 | |
| 28 <repeat name="input_files" title="Additional PepXML Input Files"> | |
| 29 <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/> | |
| 30 </repeat> | |
| 31 | |
| 32 <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--nonss"/> | |
| 33 <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--nonrs"/> | |
| 34 <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--nonse"/> | |
| 35 <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--nonsi"/> | |
| 36 <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--nonsm"/> | |
| 37 | |
| 38 <param name="minprob" type="text" label="Minimum threshod probability for reporting results"/> | |
| 39 | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data format="interprophet_pepxml" name="output" metadata_source="first_input" label="interprophet.${first_input.display_name}" from_work_dir="interprophet_output.pep.xml"/> | |
| 43 </outputs> | |
| 44 | |
| 45 <help> | |
| 46 | |
| 47 **What it does** | |
| 48 | |
| 49 Takes a set of pepXML files (possibly generated using different search engines) and calculates updated identification probabilities for each peptide. The updated probabilities are based on a statistical model that combines evidence from identifications across all of the input files, spectra, modified states and charge states. | |
| 50 | |
| 51 ---- | |
| 52 | |
| 53 **Citation** | |
| 54 | |
| 55 If you use this tool please read and cite the paper describing iProphet | |
| 56 | |
| 57 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011). | |
| 58 | |
| 59 </help> | |
| 60 | |
| 61 </tool> |