annotate idpquery.xml @ 4:66c38e74d1ae draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
author galaxyp
date Tue, 21 Nov 2017 13:19:28 -0500
parents c0e3ae85a40d
children 47c6b21c0afe
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
1 <?xml version="1.0"?>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
2 <tool id="idpquery" name="idpQuery" version="@VERSION@.0">
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
3 <description>Creates text reports from idpDB files.</description>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
4 <macros>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
5 <import>macros.xml</import>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
6 <xml name="proteinGroupByColumns">
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
7 <param name="report_columns" type="select" label="Select report columns" display="checkboxes" multiple="true">
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
8 <option value="Accession" selected="true">Accession</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
9 <option value="GeneId">Gene Id</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
10 <option value="GeneGroup">Gene Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
11 <option value="DistinctPeptides">Distinct Peptides</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
12 <option value="DistinctMatches">Distinct Matches</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
13 <option value="FilteredSpectra">Filtered Spectra</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
14 <option value="IsDecoy">Is Decoy</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
15 <option value="Cluster">Cluster</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
16 <option value="ProteinGroup">Protein Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
17 <option value="Length">Length</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
18 <option value="PercentCoverage">Percent Coverage</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
19 <option value="Sequence">Sequence</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
20 <option value="Description">Description</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
21 <option value="TaxonomyId">Taxonomy Id</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
22 <option value="GeneName">Gene Name</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
23 <option value="GeneFamily">Gene Family</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
24 <option value="Chromosome">Chromosome</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
25 <option value="GeneDescription">Gene Description</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
26 <option value="PrecursorIntensity">Precursor Intensity</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
27 <option value="PrecursorArea">Precursor Area</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
28 <option value="PrecursorBestSNR">Precursor Best SNR</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
29 <option value="PrecursorMeanSNR">Precursor Mean SNR</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
30 <option value="iTRAQ4plex">iTRAQ 4-plex</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
31 <option value="iTRAQ8plex">iTRAQ 8-plex</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
32 <option value="TMT2plex">TMT 2-plex</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
33 <option value="TMT6plex">TMT 6-plex</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
34 <option value="TMT10plex">TMT 10-plex</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
35 <option value="PivotMatchesByGroup">Pivot Matches By Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
36 <option value="PivotMatchesBySource">Pivot Matches By Source</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
37 <option value="PivotPeptidesByGroup">Pivot Peptides By Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
38 <option value="PivotPeptidesBySource">Pivot Peptides By Source</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
39 <option value="PivotSpectraByGroup">Pivot Spectra By Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
40 <option value="PivotSpectraBySource">Pivot Spectra By Source</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
41 <option value="PivotPrecursorIntensityByGroup">Pivot Precursor Intensity By Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
42 <option value="PivotPrecursorIntensityBySource">Pivot Precursor Intensity By Source</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
43 <option value="PivotPrecursorAreaByGroup">Pivot Precursor Area By Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
44 <option value="PivotPrecursorAreaBySource">Pivot Precursor Area By Source</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
45 <option value="PivotPrecursorBestSNRByGroup">Pivot Precursor Best SNR By Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
46 <option value="PivotPrecursorBestSNRBySource">Pivot Precursor Best SNR By Source</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
47 <option value="PivotPrecursorMeanSNRByGroup">Pivot Precursor Mean SNR By Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
48 <option value="PivotPrecursorMeanSNRBySource">Pivot Precursor Mean SNR By Source</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
49 <option value="PivotITRAQByGroup">Pivot iTRAQ By Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
50 <option value="PivotITRAQBySource">Pivot iTRAQ By Source</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
51 <option value="PivotTMTByGroup">Pivot TMT By Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
52 <option value="PivotTMTBySource">Pivot TMT By Source</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
53 <option value="PeptideGroups">Peptide Groups</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
54 <option value="PeptideSequences">Peptide Sequences</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
55 </param>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
56 </xml>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
57 </macros>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
58 <expand macro="requirements" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
59 <stdio>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
60 <exit_code range="1:" level="fatal" description="Job Failed" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
61 <regex match="^Error:.*$" source="both" level="fatal" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
62 </stdio>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
63 <command>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
64 <![CDATA[
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
65 #set $input_name = $input.display_name
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
66 #set $output_name = $input_name.split(".")[0] + ".tsv"
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
67 ln -s '$input' '${input_name}' &&
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
68
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
69 idpQuery $group_by.group_by_value $group_by.report_columns '${input_name}' &&
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
70 mv '$output_name' output
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
71 ]]>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
72 </command>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
73 <inputs>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
74 <param name="input" type="data" format="idpdb" label="Input idpDB" multiple="false" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
75 <conditional name="group_by">
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
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.">
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
77 <option value="Protein" selected="true">Protein</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
78 <option value="ProteinGroup">Protein Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
79 <option value="Gene">Gene</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
80 <option value="GeneGroup">Gene Group</option>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
81 </param>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
82 <when value="Protein">
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
83 <expand macro="proteinGroupByColumns" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
84 </when>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
85 <when value="ProteinGroup">
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
86 <expand macro="proteinGroupByColumns" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
87 </when>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
88 <when value="Gene">
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
89 <expand macro="proteinGroupByColumns" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
90 </when>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
91 <when value="GeneGroup">
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
92 <expand macro="proteinGroupByColumns" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
93 </when>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
94 </conditional>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
95 </inputs>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
96 <outputs>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
97 <data format="tabular" name="output" from_work_dir="output" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
98 </outputs>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
99 <tests>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
100 <test>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
101 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
102 <param name="group_by_value" value="Protein" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
103 <param name="report_columns" value="Accession,FilteredSpectra,Description" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
104 <output name="output" file="201203-624176-12-mm-gui-test-Protein-Accession,FilteredSpectra,Description.tsv" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
105 </test>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
106 <test>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
107 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
108 <param name="group_by_value" value="ProteinGroup" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
109 <param name="report_columns" value="ProteinGroup,Accession,PercentCoverage" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
110 <output name="output" file="201203-624176-12-mm-gui-test-ProteinGroup-ProteinGroup,Accession,PercentCoverage.tsv" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
111 </test>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
112 <test>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
113 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
114 <param name="group_by_value" value="Gene" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
115 <param name="report_columns" value="GeneId,Accession,DistinctPeptides" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
116 <output name="output" file="201203-624176-12-mm-gui-test-Gene-GeneId,Accession,DistinctPeptides.tsv" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
117 </test>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
118 <test>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
119 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
120 <param name="group_by_value" value="GeneGroup" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
121 <param name="report_columns" value="GeneGroup,GeneId,DistinctMatches" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
122 <output name="output" file="201203-624176-12-mm-gui-test-GeneGroup-GeneGroup,GeneId,DistinctMatches.tsv" />
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
123 </test>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
124 </tests>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
125 <help>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
126 <![CDATA[
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
127 **What it does**
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
128
1
c0e3ae85a40d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 0a0c1b53f934a0edfc7f18e9c401ad353a44092a
galaxyp
parents: 0
diff changeset
129 Creates user-configurable text reports from IDPicker 3 idpDB files.
0
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
130 ]]>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
131 </help>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
132 <citations>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
133 <citation type="doi">10.1021/pr900360j</citation>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
134 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
135 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
136 </citations>
925ec25a5436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 969d83aa6c0a170f4aa25a64718a0b2116f19fbb
galaxyp
parents:
diff changeset
137 </tool>