Mercurial > repos > nilesh > rseqc

comparison geneBody_coverage.xml @ 61:5968573462fa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author iuc
date Sat, 10 Dec 2022 11:23:05 +0000
parents 1421603cc95b
children 27e16a30667a
comparison
equal deleted inserted replaced
60:1421603cc95b 61:5968573462fa
1 <tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> 1 <tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>read coverage over gene body</description> 2 <description>read coverage over gene body</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>rseqc_macros.xml</import> 4 <import>rseqc_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <version_command><![CDATA[geneBody_coverage.py --version]]></version_command> 9 <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
10 <command><![CDATA[ 10 <command><![CDATA[
11 #if str($batch_mode.batch_mode_selector) == "merge": 11 #if str($batch_mode.batch_mode_selector) == "merge":
48 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)." /> 48 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)." />
49 <expand macro="rscript_output_param" /> 49 <expand macro="rscript_output_param" />
50 </inputs> 50 </inputs>
51 51
52 <outputs> 52 <outputs>
53 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves pdf)" /> 53 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string}: curves (PDF)" />
54 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap pdf)"> 54 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string}: heatmap (PDF)">
55 <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter> 55 <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter>
56 </data> 56 </data>
57 <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" /> 57 <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" label="${tool.name} on ${on_string}: Rscript"/>
58 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" /> 58 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string}: stats (TXT)" />
59 </outputs> 59 </outputs>
60 60
61 <!-- PDF Files contain R version, must avoid checking for diff --> 61 <!-- PDF Files contain R version, must avoid checking for diff -->
62 <tests> 62 <tests>
63 <test> 63 <test>