Mercurial > repos > galaxyp > idpquery
diff idpquery.xml @ 0:4c1e8f2243ce draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
| author | galaxyp |
|---|---|
| date | Tue, 15 Sep 2015 17:10:20 -0400 |
| parents | |
| children | 9682d5d021ab |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idpquery.xml Tue Sep 15 17:10:20 2015 -0400 @@ -0,0 +1,138 @@ +<?xml version="1.0"?> +<tool id="idpquery" name="idpQuery" version="0.1.0"> + <description>Creates text reports from idpDB files.</description> + <macros> + <xml name="proteinGroupByColumns"> + <param name="report_columns" type="select" label="Select report columns" display="checkboxes" multiple="true"> + <option value="Accession" selected="true">Accession</option> + <option value="GeneId">Gene Id</option> + <option value="GeneGroup">Gene Group</option> + <option value="DistinctPeptides">Distinct Peptides</option> + <option value="DistinctMatches">Distinct Matches</option> + <option value="FilteredSpectra">Filtered Spectra</option> + <option value="IsDecoy">Is Decoy</option> + <option value="Cluster">Cluster</option> + <option value="ProteinGroup">Protein Group</option> + <option value="Length">Length</option> + <option value="PercentCoverage">Percent Coverage</option> + <option value="Sequence">Sequence</option> + <option value="Description">Description</option> + <option value="TaxonomyId">Taxonomy Id</option> + <option value="GeneName">Gene Name</option> + <option value="GeneFamily">Gene Family</option> + <option value="Chromosome">Chromosome</option> + <option value="GeneDescription">Gene Description</option> + <option value="PrecursorIntensity">Precursor Intensity</option> + <option value="PrecursorArea">Precursor Area</option> + <option value="PrecursorBestSNR">Precursor Best SNR</option> + <option value="PrecursorMeanSNR">Precursor Mean SNR</option> + <option value="iTRAQ4plex">iTRAQ 4-plex</option> + <option value="iTRAQ8plex">iTRAQ 8-plex</option> + <option value="TMT2plex">TMT 2-plex</option> + <option value="TMT6plex">TMT 6-plex</option> + <option value="TMT10plex">TMT 10-plex</option> + <option value="PivotMatchesByGroup">Pivot Matches By Group</option> + <option value="PivotMatchesBySource">Pivot Matches By Source</option> + <option value="PivotPeptidesByGroup">Pivot Peptides By Group</option> + <option value="PivotPeptidesBySource">Pivot Peptides By Source</option> + <option value="PivotSpectraByGroup">Pivot Spectra By Group</option> + <option value="PivotSpectraBySource">Pivot Spectra By Source</option> + <option value="PivotPrecursorIntensityByGroup">Pivot Precursor Intensity By Group</option> + <option value="PivotPrecursorIntensityBySource">Pivot Precursor Intensity By Source</option> + <option value="PivotPrecursorAreaByGroup">Pivot Precursor Area By Group</option> + <option value="PivotPrecursorAreaBySource">Pivot Precursor Area By Source</option> + <option value="PivotPrecursorBestSNRByGroup">Pivot Precursor Best SNR By Group</option> + <option value="PivotPrecursorBestSNRBySource">Pivot Precursor Best SNR By Source</option> + <option value="PivotPrecursorMeanSNRByGroup">Pivot Precursor Mean SNR By Group</option> + <option value="PivotPrecursorMeanSNRBySource">Pivot Precursor Mean SNR By Source</option> + <option value="PivotITRAQByGroup">Pivot iTRAQ By Group</option> + <option value="PivotITRAQBySource">Pivot iTRAQ By Source</option> + <option value="PivotTMTByGroup">Pivot TMT By Group</option> + <option value="PivotTMTBySource">Pivot TMT By Source</option> + <option value="PeptideGroups">Peptide Groups</option> + <option value="PeptideSequences">Peptide Sequences</option> + </param> + </xml> + </macros> + <requirements> + <requirement type="package" version="3.0.8789">bumbershoot</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Job Failed" /> + <regex match="^Error:.*$" source="both" level="fatal" /> + </stdio> + <command> +<![CDATA[ + #set $input_name = $input.display_name + #set $output_name = $input_name.split(".")[0] + ".tsv" + ln -s '$input' '${input_name}' && + + idpQuery $group_by.group_by_value $group_by.report_columns '${input_name}' && + mv '$output_name' output +]]> + </command> + <inputs> + <param name="input" type="data" format="idpdb" label="Input File" multiple="false" /> + <conditional name="group_by"> + <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."> + <option value="Protein" selected="true">Protein</option> + <option value="ProteinGroup">Protein Group</option> + <option value="Gene">Gene</option> + <option value="GeneGroup">Gene Group</option> + </param> + <when value="Protein"> + <expand macro="proteinGroupByColumns" /> + </when> + <when value="ProteinGroup"> + <expand macro="proteinGroupByColumns" /> + </when> + <when value="Gene"> + <expand macro="proteinGroupByColumns" /> + </when> + <when value="GeneGroup"> + <expand macro="proteinGroupByColumns" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="output" from_work_dir="output" /> + </outputs> + <tests> + <test> + <param name="input" value="201203-624176-12-mm-gui-test.idpDB" /> + <param name="group_by_value" value="Protein" /> + <param name="report_columns" value="Accession,FilteredSpectra,Description" /> + <output name="output" file="201203-624176-12-mm-gui-test-Protein-Accession,FilteredSpectra,Description.tsv" /> + </test> + <test> + <param name="input" value="201203-624176-12-mm-gui-test.idpDB" /> + <param name="group_by_value" value="ProteinGroup" /> + <param name="report_columns" value="ProteinGroup,Accession,PercentCoverage" /> + <output name="output" file="201203-624176-12-mm-gui-test-ProteinGroup-ProteinGroup,Accession,PercentCoverage.tsv" /> + </test> + <test> + <param name="input" value="201203-624176-12-mm-gui-test.idpDB" /> + <param name="group_by_value" value="Gene" /> + <param name="report_columns" value="GeneId,Accession,DistinctPeptides" /> + <output name="output" file="201203-624176-12-mm-gui-test-Gene-GeneId,Accession,DistinctPeptides.tsv" /> + </test> + <test> + <param name="input" value="201203-624176-12-mm-gui-test.idpDB" /> + <param name="group_by_value" value="GeneGroup" /> + <param name="report_columns" value="GeneGroup,GeneId,DistinctMatches" /> + <output name="output" file="201203-624176-12-mm-gui-test-GeneGroup-GeneGroup,GeneId,DistinctMatches.tsv" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Creates user-configurable text reports from IDPicker 3 idpDB files. +]]> + </help> + <citations> + <citation type="doi">10.1021/pr900360j</citation> + <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, + year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> + </citations> +</tool> \ No newline at end of file