Mercurial > repos > nilesh > rseqc

comparison geneBody_coverage2.xml @ 59:dbedfc5f5a3c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
author iuc
date Sat, 18 Dec 2021 19:41:19 +0000
parents daae0a118c36
children 1421603cc95b
comparison
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58:1a052c827e88 59:dbedfc5f5a3c
1 <tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@WRAPPER_VERSION@.1"> 1 <tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@TOOL_VERSION@.2">
2 <description> 2 <description>
3 Read coverage over gene body 3 Read coverage over gene body
4 </description> 4 </description>
5 5 <expand macro="bio_tools"/>
6 <macros> 6 <macros>
7 <import>rseqc_macros.xml</import> 7 <import>rseqc_macros.xml</import>
8 </macros> 8 </macros>
9 9
10 <expand macro="requirements" /> 10 <expand macro="requirements" />
19 </command> 19 </command>
20 20
21 <inputs> 21 <inputs>
22 <param name="input" type="data" label="Input bigwig file" format="bigwig" /> 22 <param name="input" type="data" label="Input bigwig file" format="bigwig" />
23 <expand macro="refgene_param" /> 23 <expand macro="refgene_param" />
24 <expand macro="rscript_output_param" />
24 </inputs> 25 </inputs>
25 26
26 <outputs> 27 <outputs>
27 <expand macro="pdf_output_data" filename="output.geneBodyCoverage.pdf" /> 28 <expand macro="pdf_output_data" filename="output.geneBodyCoverage.pdf" />
28 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" /> 29 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" />
29 <expand macro="rscript_output_data" filename="output.geneBodyCoverage_plot.r" /> 30 <expand macro="rscript_output_data" filename="output.geneBodyCoverage_plot.r" />
30 </outputs> 31 </outputs>
31 32
32 <tests> 33 <tests>
33 <test> 34 <test expect_num_outputs="3">
34 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig" /> 35 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig" />
35 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> 36 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
36 <param name="rscript_output" value="true" /> 37 <param name="rscript_output" value="true" />
37 <output name="outputpdf" file="output.geneBodyCoverage2.curves.pdf" compare="sim_size" /> 38 <output name="outputpdf" file="output.geneBodyCoverage2.curves.pdf" compare="sim_size" />
38 <output name="outputr" file="output.geneBodyCoverage2.r" /> 39 <output name="outputr" file="output.geneBodyCoverage2_r" />
39 <output name="outputtxt" file="output.geneBodyCoverage2.txt" /> 40 <output name="outputtxt" file="output.geneBodyCoverage2.txt" />
40 </test> 41 </test>
41 </tests> 42 </tests>
42 43
43 <help><![CDATA[ 44 <help><![CDATA[