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comparison interprophet.xml @ 2:418f42b34049 draft

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Reuploading
author iracooke
date Mon, 23 Jul 2012 00:20:58 -0400
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1:deaedec14cc8 2:418f42b34049
1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.0">
2 <requirements><requirement type="package">protk</requirement></requirements>
3 <description>Combine Peptide Prophet results from multiple search engines</description>
4
5 <command interpreter="ruby">
6
7 interprophet_wrapper.rb $output $use_nss $use_nrs $use_nse $use_nsi $use_nsm --minprob $minprob
8
9
10 ## Inputs.
11 ${first_input}
12 #for $input_file in $input_files:
13 ${input_file.additional_input}
14 #end for
15
16 </command>
17
18 <inputs>
19
20 <param name="first_input" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
21
22 <repeat name="input_files" title="Additional PepXML Input Files">
23 <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/>
24 </repeat>
25
26 <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--nonss"/>
27 <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--nonrs"/>
28 <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--nonse"/>
29 <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--nonsi"/>
30 <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--nonsm"/>
31
32 <param name="minprob" type="text" label="Minimum threshod probability for reporting results"/>
33
34 </inputs>
35 <outputs>
36 <data format="interprophet_pepxml" name="output" metadata_source="first_input" label="interprophet.${first_input.display_name}" from_work_dir="interprophet_output.pep.xml"/>
37 </outputs>
38
39 <help>
40
41 **What it does**
42
43 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.
44
45 ----
46
47 **Citation**
48
49 If you use this tool please read and cite the paper describing iProphet
50
51 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011).
52
53 </help>
54
55 </tool>