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comparison interprophet.xml @ 14:d90c8bc10a9c draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 19:55:19 -0400
parents 4c66453a168e
children 0746a2ae9e04
comparison
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13:b793fe628648 14:d90c8bc10a9c
1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1"> 1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.0">
2 2
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3">protk</requirement> 4 <container type="docker">iracooke/protk-1.4.1</container>
5 <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> 5 <requirement type="package" version="1.4">protk</requirement>
6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
6 </requirements> 7 </requirements>
7 8
8 9
9 <description>Combine Peptide Prophet results from multiple search engines</description> 10 <description>Combine Peptide Prophet results from multiple search engines</description>
10 11
20 21
21 $use_nsi 22 $use_nsi
22 23
23 $use_nsm 24 $use_nsm
24 25
25 --minprob $minprob 26 --p-thresh $p_thresh
26 27
27 ## Inputs. 28 --threads $threads
28 ${first_input} 29
29 #for $input_file in $input_files: 30 #for $pepxml_file in $pepxml_files:
30 ${input_file.additional_input} 31 ${pepxml_file}
31 #end for 32 #end for
32 33
33 </command> 34 </command>
34 35
36
35 <inputs> 37 <inputs>
36 38
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"/> 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"/>
38 40
39 <repeat name="input_files" title="Additional PepXML Input Files"> 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"/>
40 <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/> 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"/>
41 </repeat> 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"/>
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"/>
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"/>
42 46
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"/> 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"/>
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"/> 48
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"/> 49 <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
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 50
51 </inputs> 51 </inputs>
52 <outputs> 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"/> 53 <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/>
54 </outputs> 54 </outputs>
55 55
56 <help> 56 <help>
57 57
58 **What it does** 58 **What it does**