|
7
|
1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1">
|
|
2
|
2
|
|
|
3 <requirements>
|
|
8
|
4 <requirement type="package" version="1.2.2">galaxy_protk</requirement>
|
|
2
|
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
|
|
8
|
11 <command interpreter="bash">
|
|
|
12
|
|
|
13 interprophet_wrapper.sh
|
|
|
14
|
|
|
15 $output
|
|
|
16
|
|
|
17 $use_nss
|
|
2
|
18
|
|
8
|
19 $use_nrs
|
|
|
20
|
|
|
21 $use_nse
|
|
2
|
22
|
|
8
|
23 $use_nsi
|
|
|
24
|
|
|
25 $use_nsm
|
|
|
26
|
|
|
27 --minprob $minprob
|
|
2
|
28
|
|
|
29 ## Inputs.
|
|
|
30 ${first_input}
|
|
|
31 #for $input_file in $input_files:
|
|
|
32 ${input_file.additional_input}
|
|
|
33 #end for
|
|
|
34
|
|
|
35 </command>
|
|
|
36
|
|
|
37 <inputs>
|
|
|
38
|
|
|
39 <param name="first_input" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
|
|
|
40
|
|
|
41 <repeat name="input_files" title="Additional PepXML Input Files">
|
|
|
42 <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/>
|
|
|
43 </repeat>
|
|
|
44
|
|
8
|
45 <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--no-nss"/>
|
|
|
46 <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--no-nrs"/>
|
|
|
47 <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--no-nse"/>
|
|
|
48 <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--no-nsi"/>
|
|
|
49 <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--no-nsm"/>
|
|
2
|
50
|
|
|
51 <param name="minprob" type="text" label="Minimum threshod probability for reporting results"/>
|
|
|
52
|
|
|
53 </inputs>
|
|
|
54 <outputs>
|
|
|
55 <data format="interprophet_pepxml" name="output" metadata_source="first_input" label="interprophet.${first_input.display_name}" from_work_dir="interprophet_output.pep.xml"/>
|
|
|
56 </outputs>
|
|
|
57
|
|
|
58 <help>
|
|
|
59
|
|
|
60 **What it does**
|
|
|
61
|
|
|
62 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.
|
|
|
63
|
|
|
64 ----
|
|
|
65
|
|
|
66 **Citation**
|
|
|
67
|
|
|
68 If you use this tool please read and cite the paper describing iProphet
|
|
|
69
|
|
|
70 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011).
|
|
|
71
|
|
|
72 </help>
|
|
|
73
|
|
|
74 </tool>
|
