Mercurial > repos > nilesh > rseqc
diff junction_annotation.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/junction_annotation.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/junction_annotation.xml Tue Apr 09 11:24:55 2024 +0000 @@ -3,9 +3,7 @@ <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - <expand macro="requirements"> <!-- Required due to conda solver bug: https://github.com/conda/conda/issues/6269 @@ -13,11 +11,8 @@ --> <requirement type="package" version="4.2.2">r-base</requirement> </expand> - - <expand macro="stdio" /> - + <expand macro="stdio"/> <version_command><![CDATA[junction_annotation.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ junction_annotation.py @@ -29,36 +24,32 @@ 2> >(tee -a stats.txt >&2) ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="refgene_param" /> - <expand macro="min_intron_param" /> - <expand macro="mapq_param" /> - <expand macro="rscript_output_param" /> + <expand macro="bam_sam_param"/> + <expand macro="refgene_param"/> + <expand macro="min_intron_param"/> + <expand macro="mapq_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/> - <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)" /> - <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)" /> + <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)"/> + <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)"/> <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/> - <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats" /> + <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> + <test expect_num_outputs="5"> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> - <param name="rscript_output" value="true" /> + <param name="rscript_output" value="true"/> <output name="outputxls" file="output.junction.xls" ftype="tabular"/> - <output name="outputr" file="output.junction_plot_r" /> - <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" /> - <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" /> - <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2" /> + <output name="outputr" file="output.junction_plot_r"/> + <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size"/> + <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size"/> + <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2"/> </test> </tests> - <help><![CDATA[ junction_annotation.py ++++++++++++++++++++++ @@ -112,7 +103,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>