annotate interprophet.xml @ 14:d90c8bc10a9c draft

Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 19:55:19 -0400
parents 4c66453a168e
children 0746a2ae9e04
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.0">
12
4c66453a168e Uploaded
iracooke
parents:
diff changeset
2
4c66453a168e Uploaded
iracooke
parents:
diff changeset
3 <requirements>
14
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
4 <container type="docker">iracooke/protk-1.4.1</container>
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
5 <requirement type="package" version="1.4">protk</requirement>
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
12
4c66453a168e Uploaded
iracooke
parents:
diff changeset
7 </requirements>
4c66453a168e Uploaded
iracooke
parents:
diff changeset
8
4c66453a168e Uploaded
iracooke
parents:
diff changeset
9
4c66453a168e Uploaded
iracooke
parents:
diff changeset
10 <description>Combine Peptide Prophet results from multiple search engines</description>
4c66453a168e Uploaded
iracooke
parents:
diff changeset
11
4c66453a168e Uploaded
iracooke
parents:
diff changeset
12 <command>interprophet.rb --galaxy
4c66453a168e Uploaded
iracooke
parents:
diff changeset
13
4c66453a168e Uploaded
iracooke
parents:
diff changeset
14 -o interprophet_output.pep.xml
4c66453a168e Uploaded
iracooke
parents:
diff changeset
15
4c66453a168e Uploaded
iracooke
parents:
diff changeset
16 $use_nss
4c66453a168e Uploaded
iracooke
parents:
diff changeset
17
4c66453a168e Uploaded
iracooke
parents:
diff changeset
18 $use_nrs
4c66453a168e Uploaded
iracooke
parents:
diff changeset
19
4c66453a168e Uploaded
iracooke
parents:
diff changeset
20 $use_nse
4c66453a168e Uploaded
iracooke
parents:
diff changeset
21
4c66453a168e Uploaded
iracooke
parents:
diff changeset
22 $use_nsi
4c66453a168e Uploaded
iracooke
parents:
diff changeset
23
4c66453a168e Uploaded
iracooke
parents:
diff changeset
24 $use_nsm
4c66453a168e Uploaded
iracooke
parents:
diff changeset
25
14
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
26 --p-thresh $p_thresh
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
27
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
28 --threads $threads
12
4c66453a168e Uploaded
iracooke
parents:
diff changeset
29
14
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
30 #for $pepxml_file in $pepxml_files:
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
31 ${pepxml_file}
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
32 #end for
12
4c66453a168e Uploaded
iracooke
parents:
diff changeset
33
4c66453a168e Uploaded
iracooke
parents:
diff changeset
34 </command>
4c66453a168e Uploaded
iracooke
parents:
diff changeset
35
14
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
36
12
4c66453a168e Uploaded
iracooke
parents:
diff changeset
37 <inputs>
4c66453a168e Uploaded
iracooke
parents:
diff changeset
38
14
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
39 <param name="pepxml_files" multiple="true" 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"/>
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
40
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
41 <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" falsevalue="--no-nss"/>
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
42 <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="" falsevalue="--no-nrs"/>
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
43 <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="" falsevalue="--no-nse"/>
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
44 <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="" falsevalue="--no-nsi"/>
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
45 <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="" falsevalue="--no-nsm"/>
12
4c66453a168e Uploaded
iracooke
parents:
diff changeset
46
14
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
47 <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
48
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
49 <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
12
4c66453a168e Uploaded
iracooke
parents:
diff changeset
50
4c66453a168e Uploaded
iracooke
parents:
diff changeset
51 </inputs>
4c66453a168e Uploaded
iracooke
parents:
diff changeset
52 <outputs>
14
d90c8bc10a9c Docker support and update for protk 1.4
iracooke
parents: 12
diff changeset
53 <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/>
12
4c66453a168e Uploaded
iracooke
parents:
diff changeset
54 </outputs>
4c66453a168e Uploaded
iracooke
parents:
diff changeset
55
4c66453a168e Uploaded
iracooke
parents:
diff changeset
56 <help>
4c66453a168e Uploaded
iracooke
parents:
diff changeset
57
4c66453a168e Uploaded
iracooke
parents:
diff changeset
58 **What it does**
4c66453a168e Uploaded
iracooke
parents:
diff changeset
59
4c66453a168e Uploaded
iracooke
parents:
diff changeset
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.
4c66453a168e Uploaded
iracooke
parents:
diff changeset
61
4c66453a168e Uploaded
iracooke
parents:
diff changeset
62 ----
4c66453a168e Uploaded
iracooke
parents:
diff changeset
63
4c66453a168e Uploaded
iracooke
parents:
diff changeset
64 **Citation**
4c66453a168e Uploaded
iracooke
parents:
diff changeset
65
4c66453a168e Uploaded
iracooke
parents:
diff changeset
66 If you use this tool please read and cite the paper describing iProphet
4c66453a168e Uploaded
iracooke
parents:
diff changeset
67
4c66453a168e Uploaded
iracooke
parents:
diff changeset
68 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011).
4c66453a168e Uploaded
iracooke
parents:
diff changeset
69
4c66453a168e Uploaded
iracooke
parents:
diff changeset
70 </help>
4c66453a168e Uploaded
iracooke
parents:
diff changeset
71
4c66453a168e Uploaded
iracooke
parents:
diff changeset
72 </tool>