Mercurial > repos > iracooke > tpp_prophets
comparison interprophet.xml @ 12:4c66453a168e draft
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author | iracooke |
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date | Mon, 16 Jun 2014 07:17:09 -0400 |
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children | d90c8bc10a9c |
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11:8512f117b10b | 12:4c66453a168e |
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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> |