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comparison interprophet.xml @ 15:0746a2ae9e04 draft

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:45:24 -0400
parents d90c8bc10a9c
children 1b86e378de37
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14:d90c8bc10a9c 15:0746a2ae9e04
1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.0"> 1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.1">
2 2 <description>Combine Peptide Prophet results from multiple search engines</description>
3 <requirements> 3 <requirements>
4 <container type="docker">iracooke/protk-1.4.1</container> 4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="1.4">protk</requirement> 5 <requirement type="package" version="1.4.3">protk</requirement>
6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> 6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
7 </requirements> 7 </requirements>
8 <command>
9 <![CDATA[
10 interprophet.rb --galaxy
11 #if str( $input_type.type ) == "files":
12 #for $pepxml_file in $input_type.pepxml_files:
13 ${pepxml_file}
14 #end for
15 #else
16 #for $list_item in $input_type.pepxml_list:
17 ${list_item}
18 #end for
19 #for $extra_list_holder in $input_type.extra_pepxml_lists:
20 #for $list_item in $extra_list_holder.extra_list:
21 ${list_item}
22 #end for
23 #end for
24 #end if
8 25
26 -o interprophet_output.pep.xml
27 $use_nss
28 $use_nrs
29 $use_nse
30 $use_nsi
31 $use_nsm
32 --p-thresh $p_thresh
33 --threads "\${GALAXY_SLOTS:-12}"
9 34
10 <description>Combine Peptide Prophet results from multiple search engines</description> 35 ]]>
36 </command>
37 <inputs>
11 38
12 <command>interprophet.rb --galaxy 39 <conditional name="input_type">
40 <param name="type" type="select" label="Input Type">
41 <option value="files" selected="true">Datasets</option>
42 <option value="collections">Collections</option>
43 </param>
44 <when value="files">
45 <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"/>
46 </when>
47 <when value="collections">
48 <param name="pepxml_list" type="data_collection" multiple="true" collection_type="list" 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"/>
49 <repeat name="extra_pepxml_lists" title="Additional PepXML Collections" >
50 <param name="extra_list" type="data_collection" multiple="true" collection_type="list" 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"/>
51 </repeat>
52 </when>
53 </conditional>
13 54
14 -o interprophet_output.pep.xml 55 <!-- <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"/> -->
15 56
16 $use_nss 57 <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"/>
58 <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"/>
59 <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"/>
60 <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"/>
61 <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"/>
62 <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"/>
17 63
18 $use_nrs 64 </inputs>
19 65 <outputs>
20 $use_nse 66 <data format="interprophet_pepxml" name="output" from_work_dir="interprophet_output.pep.xml"/>
21 67 </outputs>
22 $use_nsi 68 <help>
23
24 $use_nsm
25
26 --p-thresh $p_thresh
27
28 --threads $threads
29
30 #for $pepxml_file in $pepxml_files:
31 ${pepxml_file}
32 #end for
33
34 </command>
35
36
37 <inputs>
38
39 <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
40
41 <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" falsevalue="--no-nss"/>
42 <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="" falsevalue="--no-nrs"/>
43 <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="" falsevalue="--no-nse"/>
44 <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="" falsevalue="--no-nsi"/>
45 <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="" falsevalue="--no-nsm"/>
46
47 <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
48
49 <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
50
51 </inputs>
52 <outputs>
53 <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/>
54 </outputs>
55
56 <help>
57 69
58 **What it does** 70 **What it does**
59 71
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. 72 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 73
65 77
66 If you use this tool please read and cite the paper describing iProphet 78 If you use this tool please read and cite the paper describing iProphet
67 79
68 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011). 80 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011).
69 81
70 </help> 82 </help>
71
72 </tool> 83 </tool>