Mercurial > repos > lparsons > rseqc

comparison geneBody_coverage.xml @ 1:cd2daa987b69 draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
author lparsons
date Tue, 07 Jul 2015 14:14:04 -0400
parents 306127635959
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0:306127635959 1:cd2daa987b69
34 geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output 34 geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output
35 ]]> 35 ]]>
36 </command> 36 </command>
37 37
38 <inputs> 38 <inputs>
39 <param name="input" type="data" label="Additional input .bam files" format="bam" /> 39 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
40 <repeat name="additionalinputs" title="Input .bam file"> 40 <repeat name="additionalinputs" title="Additional input .bam files">
41 <param name="file" type="data" label="Input .bam file" format="bam" /> 41 <param name="file" type="data" label="Additional input .bam file" format="bam" />
42 </repeat> 42 </repeat>
43 <param name="refgene" type="data" label="Reference Genome" format="bed" /> 43 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
44 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length" help="Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100)." /> 44 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length in bp (default: 100)" help="mRNA that are shorter than this value will be skipped (--minimum_length)." />
45 </inputs> 45 </inputs>
46 46
47 <outputs> 47 <outputs>
48 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves PDF)" /> 48 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves PDF)" />
49 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap PDF)"> 49 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap PDF)">