Mercurial > repos > iracooke > tpp_prophets

comparison interprophet.xml @ 12:4c66453a168e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iracooke
date Mon, 16 Jun 2014 07:17:09 -0400
parents
children d90c8bc10a9c
comparison
equal deleted inserted replaced
11:8512f117b10b 12:4c66453a168e
1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1">
2
3 <requirements>
4 <requirement type="package" version="1.3">protk</requirement>
5 <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement>
6 </requirements>
7
8
9 <description>Combine Peptide Prophet results from multiple search engines</description>
10
11 <command>interprophet.rb --galaxy
12
13 -o interprophet_output.pep.xml
14
15 $use_nss
16
17 $use_nrs
18
19 $use_nse
20
21 $use_nsi
22
23 $use_nsm
24
25 --minprob $minprob
26
27 ## Inputs.
28 ${first_input}
29 #for $input_file in $input_files:
30 ${input_file.additional_input}
31 #end for
32
33 </command>
34
35 <inputs>
36
37 <param name="first_input" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
38
39 <repeat name="input_files" title="Additional PepXML Input Files">
40 <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/>
41 </repeat>
42
43 <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--no-nss"/>
44 <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--no-nrs"/>
45 <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--no-nse"/>
46 <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--no-nsi"/>
47 <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--no-nsm"/>
48
49 <param name="minprob" type="text" label="Minimum threshod probability for reporting results"/>
50
51 </inputs>
52 <outputs>
53 <data format="interprophet_pepxml" name="output" metadata_source="first_input" label="interprophet.${first_input.display_name}" from_work_dir="interprophet_output.pep.xml"/>
54 </outputs>
55
56 <help>
57
58 **What it does**
59
60 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.
61
62 ----
63
64 **Citation**
65
66 If you use this tool please read and cite the paper describing iProphet
67
68 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011).
69
70 </help>
71
72 </tool>