Mercurial > repos > nilesh > rseqc
diff geneBody_coverage.xml @ 32:580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
| author | lparsons |
|---|---|
| date | Mon, 07 Oct 2013 15:01:13 -0400 |
| parents | cc5eaa9376d8 |
| children |
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--- a/geneBody_coverage.xml Wed Oct 02 02:20:04 2013 -0400 +++ b/geneBody_coverage.xml Mon Oct 07 15:01:13 2013 -0400 @@ -1,29 +1,29 @@ -<tool id="geneBody_coverage" name="Gene Body Converage (BAM)" version="1.1"> - <description> - Read coverage over gene body. - </description> - <requirements> - <requirement type="package" version="2.11.0">R</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="2.3.7">rseqc</requirement> - </requirements> - <command> - geneBody_coverage.py -i $input -r $refgene -o output - </command> - <inputs> - <param name="input" type="data" label="Input .bam file" format="bam" /> - <param name="refgene" type="data" label="Reference Genome" format="bed" /> - </inputs> - <outputs> - <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" /> - <data name="outputr" format="r" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" /> - <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" /> - </outputs> +<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="1.1"> + <description> + Read coverage over gene body. + </description> + <requirements> + <requirement type="package" version="3.0.1">R</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="2.3.7">rseqc</requirement> + </requirements> + <command> + geneBody_coverage.py -i $input -r $refgene -o output + </command> <stdio> <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> </stdio> - <help> + <inputs> + <param name="input" type="data" label="Input .bam file" format="bam" /> + <param name="refgene" type="data" label="Reference Genome" format="bed" /> + </inputs> + <outputs> + <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" /> + <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" /> + <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" /> + </outputs> + <help> geneBody_coverage.py ++++++++++++++++++++ @@ -54,7 +54,7 @@ .. image:: http://rseqc.sourceforge.net/_images/geneBody_coverage.png :height: 600 px :width: 600 px - :scale: 80 % + :scale: 80 % -----