Mercurial > repos > nilesh > rseqc
diff clipping_profile.xml @ 63:27e16a30667a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
| author | iuc |
|---|---|
| date | Tue, 09 Apr 2024 11:24:55 +0000 |
| parents | 473382134e56 |
| children |
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--- a/clipping_profile.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/clipping_profile.xml Tue Apr 09 11:24:55 2024 +0000 @@ -5,49 +5,40 @@ <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[clipping_profile.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ clipping_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}" ]]> </command> - <inputs> - <expand macro="bam_param" /> - <expand macro="mapq_param" /> - <expand macro="layout_param" /> - <expand macro="rscript_output_param" /> + <expand macro="bam_param"/> + <expand macro="mapq_param"/> + <expand macro="layout_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" label="${tool.name} on ${on_string}: PDF"/> <expand macro="xls_output_data" filename="output.clipping_profile.xls" label="${tool.name} on ${on_string}: XML"/> <expand macro="rscript_output_data" filename="output.clipping_profile.r" label="${tool.name} on ${on_string}: Rscript"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" /> + <test expect_num_outputs="2"> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size"/> <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/> </test> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - <param name="rscript_output" value="true" /> - <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" /> + <test expect_num_outputs="3"> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <param name="rscript_output" value="true"/> + <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size"/> <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/> - <output name="outputr" file="output.clipping_profile_r" /> + <output name="outputr" file="output.clipping_profile_r"/> </test> </tests> - <help><![CDATA[ clipping_profile.py +++++++++++++++++++ @@ -81,7 +72,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>