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comparison idpquery.xml @ 0:925ec25a5436 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
author galaxyp
date Wed, 23 Aug 2017 19:11:08 -0400
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children c0e3ae85a40d
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1 <?xml version="1.0"?>
2 <tool id="idpquery" name="idpQuery" version="@VERSION@.0">
3 <description>Creates text reports from idpDB files.</description>
4 <macros>
5 <import>macros.xml</import>
6 <xml name="proteinGroupByColumns">
7 <param name="report_columns" type="select" label="Select report columns" display="checkboxes" multiple="true">
8 <option value="Accession" selected="true">Accession</option>
9 <option value="GeneId">Gene Id</option>
10 <option value="GeneGroup">Gene Group</option>
11 <option value="DistinctPeptides">Distinct Peptides</option>
12 <option value="DistinctMatches">Distinct Matches</option>
13 <option value="FilteredSpectra">Filtered Spectra</option>
14 <option value="IsDecoy">Is Decoy</option>
15 <option value="Cluster">Cluster</option>
16 <option value="ProteinGroup">Protein Group</option>
17 <option value="Length">Length</option>
18 <option value="PercentCoverage">Percent Coverage</option>
19 <option value="Sequence">Sequence</option>
20 <option value="Description">Description</option>
21 <option value="TaxonomyId">Taxonomy Id</option>
22 <option value="GeneName">Gene Name</option>
23 <option value="GeneFamily">Gene Family</option>
24 <option value="Chromosome">Chromosome</option>
25 <option value="GeneDescription">Gene Description</option>
26 <option value="PrecursorIntensity">Precursor Intensity</option>
27 <option value="PrecursorArea">Precursor Area</option>
28 <option value="PrecursorBestSNR">Precursor Best SNR</option>
29 <option value="PrecursorMeanSNR">Precursor Mean SNR</option>
30 <option value="iTRAQ4plex">iTRAQ 4-plex</option>
31 <option value="iTRAQ8plex">iTRAQ 8-plex</option>
32 <option value="TMT2plex">TMT 2-plex</option>
33 <option value="TMT6plex">TMT 6-plex</option>
34 <option value="TMT10plex">TMT 10-plex</option>
35 <option value="PivotMatchesByGroup">Pivot Matches By Group</option>
36 <option value="PivotMatchesBySource">Pivot Matches By Source</option>
37 <option value="PivotPeptidesByGroup">Pivot Peptides By Group</option>
38 <option value="PivotPeptidesBySource">Pivot Peptides By Source</option>
39 <option value="PivotSpectraByGroup">Pivot Spectra By Group</option>
40 <option value="PivotSpectraBySource">Pivot Spectra By Source</option>
41 <option value="PivotPrecursorIntensityByGroup">Pivot Precursor Intensity By Group</option>
42 <option value="PivotPrecursorIntensityBySource">Pivot Precursor Intensity By Source</option>
43 <option value="PivotPrecursorAreaByGroup">Pivot Precursor Area By Group</option>
44 <option value="PivotPrecursorAreaBySource">Pivot Precursor Area By Source</option>
45 <option value="PivotPrecursorBestSNRByGroup">Pivot Precursor Best SNR By Group</option>
46 <option value="PivotPrecursorBestSNRBySource">Pivot Precursor Best SNR By Source</option>
47 <option value="PivotPrecursorMeanSNRByGroup">Pivot Precursor Mean SNR By Group</option>
48 <option value="PivotPrecursorMeanSNRBySource">Pivot Precursor Mean SNR By Source</option>
49 <option value="PivotITRAQByGroup">Pivot iTRAQ By Group</option>
50 <option value="PivotITRAQBySource">Pivot iTRAQ By Source</option>
51 <option value="PivotTMTByGroup">Pivot TMT By Group</option>
52 <option value="PivotTMTBySource">Pivot TMT By Source</option>
53 <option value="PeptideGroups">Peptide Groups</option>
54 <option value="PeptideSequences">Peptide Sequences</option>
55 </param>
56 </xml>
57 </macros>
58 <expand macro="requirements" />
59 <stdio>
60 <exit_code range="1:" level="fatal" description="Job Failed" />
61 <regex match="^Error:.*$" source="both" level="fatal" />
62 </stdio>
63 <command>
64 <![CDATA[
65 #set $input_name = $input.display_name
66 #set $output_name = $input_name.split(".")[0] + ".tsv"
67 ln -s '$input' '${input_name}' &&
68
69 idpQuery $group_by.group_by_value $group_by.report_columns '${input_name}' &&
70 mv '$output_name' output
71 ]]>
72 </command>
73 <inputs>
74 <param name="input" type="data" format="idpdb" label="Input idpDB" multiple="false" />
75 <conditional name="group_by">
76 <param name="group_by_value" type="select" label="What proteomic entity do you want to group by?" help="Only protein- and gene-centric entities are currently supported.">
77 <option value="Protein" selected="true">Protein</option>
78 <option value="ProteinGroup">Protein Group</option>
79 <option value="Gene">Gene</option>
80 <option value="GeneGroup">Gene Group</option>
81 </param>
82 <when value="Protein">
83 <expand macro="proteinGroupByColumns" />
84 </when>
85 <when value="ProteinGroup">
86 <expand macro="proteinGroupByColumns" />
87 </when>
88 <when value="Gene">
89 <expand macro="proteinGroupByColumns" />
90 </when>
91 <when value="GeneGroup">
92 <expand macro="proteinGroupByColumns" />
93 </when>
94 </conditional>
95 </inputs>
96 <outputs>
97 <data format="tabular" name="output" from_work_dir="output" />
98 </outputs>
99 <tests>
100 <test>
101 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" />
102 <param name="group_by_value" value="Protein" />
103 <param name="report_columns" value="Accession,FilteredSpectra,Description" />
104 <output name="output" file="201203-624176-12-mm-gui-test-Protein-Accession,FilteredSpectra,Description.tsv" />
105 </test>
106 <test>
107 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" />
108 <param name="group_by_value" value="ProteinGroup" />
109 <param name="report_columns" value="ProteinGroup,Accession,PercentCoverage" />
110 <output name="output" file="201203-624176-12-mm-gui-test-ProteinGroup-ProteinGroup,Accession,PercentCoverage.tsv" />
111 </test>
112 <test>
113 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" />
114 <param name="group_by_value" value="Gene" />
115 <param name="report_columns" value="GeneId,Accession,DistinctPeptides" />
116 <output name="output" file="201203-624176-12-mm-gui-test-Gene-GeneId,Accession,DistinctPeptides.tsv" />
117 </test>
118 <test>
119 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" />
120 <param name="group_by_value" value="GeneGroup" />
121 <param name="report_columns" value="GeneGroup,GeneId,DistinctMatches" />
122 <output name="output" file="201203-624176-12-mm-gui-test-GeneGroup-GeneGroup,GeneId,DistinctMatches.tsv" />
123 </test>
124 </tests>
125 <help>
126 <![CDATA[
127 **What it does**
128
129 Creates user-configurable text reports from IDPicker 3 idpDB files.
130 ]]>
131 </help>
132 <citations>
133 <citation type="doi">10.1021/pr900360j</citation>
134 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
135 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
136 </citations>
137 </tool>