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comparison interprophet.xml @ 2:25261529840c

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author iracooke
date Mon, 04 Mar 2013 17:11:46 -0500
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1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.0">
2
3 <requirements>
4 <requirement type="package" version="1.1.9">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>