Mercurial > repos > iracooke > tpp_prophets

annotate interprophet.xml @ 18:84b47300a4c8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 20:46:16 -0400
parents b68f292b2904
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.1">
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
2 <description>Combine Peptide Prophet results from multiple search engines</description>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
3 <requirements>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
4 <container type="docker">iracooke/protk-1.4.3</container>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
5 <requirement type="package" version="1.4.3">protk</requirement>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
7 </requirements>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
8 <command>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
9 <![CDATA[
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
10 interprophet.rb --galaxy
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
11 #if str( $input_type.type ) == "files":
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
12 #for $pepxml_file in $input_type.pepxml_files:
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
13 ${pepxml_file}
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
14 #end for
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
15 #else
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
16 #for $list_item in $input_type.pepxml_list:
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
17 ${list_item}
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
18 #end for
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
19 #for $extra_list_holder in $input_type.extra_pepxml_lists:
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
20 #for $list_item in $extra_list_holder.extra_list:
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
21 ${list_item}
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
22 #end for
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
23 #end for
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
24 #end if
17
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
25
18
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
26 -o interprophet_output.pep.xml
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
27 $use_nss
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
28 $use_nrs
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
29 $use_nse
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
30 $use_nsi
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
31 $use_nsm
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
32 --p-thresh $p_thresh
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
33 --threads "\${GALAXY_SLOTS:-12}"
17
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
34
18
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
35 ]]>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
36 </command>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
37 <inputs>
17
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
38
18
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
39 <conditional name="input_type">
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
40 <param name="type" type="select" label="Input Type">
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
41 <option value="files" selected="true">Datasets</option>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
42 <option value="collections">Collections</option>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
43 </param>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
44 <when value="files">
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
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"/>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
46 </when>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
47 <when value="collections">
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
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"/>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
49 <repeat name="extra_pepxml_lists" title="Additional PepXML Collections" >
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
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"/>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
51 </repeat>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
52 </when>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
53 </conditional>
17
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
54
18
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
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"/> -->
17
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
56
18
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
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"/>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
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"/>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
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"/>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
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"/>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
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"/>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
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"/>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
63
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
64 </inputs>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
65 <outputs>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
66 <data format="interprophet_pepxml" name="output" from_work_dir="interprophet_output.pep.xml"/>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
67 </outputs>
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
68 <help>
17
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
69
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
70 **What it does**
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
71
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
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.
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
73
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
74 ----
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
75
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
76 **Citation**
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
77
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
78 If you use this tool please read and cite the paper describing iProphet
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
79
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
80 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011).
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
81
18
84b47300a4c8 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 17
diff changeset
82 </help>
17
b68f292b2904 Uploaded
simonalpha
parents:
diff changeset
83 </tool>