Mercurial > repos > nilesh > rseqc
diff RPKM_saturation.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/RPKM_saturation.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/RPKM_saturation.xml Tue Apr 09 11:24:55 2024 +0000 @@ -4,13 +4,9 @@ <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[RPKM_saturation.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ RPKM_saturation.py -i 'input.${extension}' -o output -r '${refgene}' @@ -36,53 +32,49 @@ -l ${percentileFloor} -u ${percentileCeiling} -s ${percentileStep} -c ${rpkmCutoff} --mapq $mapq ]]></command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="refgene_param" /> - <expand macro="strand_type_param" /> + <expand macro="bam_sam_param"/> + <expand macro="refgene_param"/> + <expand macro="strand_type_param"/> <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/> - <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)" /> - <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)" /> - <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)" /> - <expand macro="mapq_param" /> - <expand macro="rscript_output_param" /> + <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)"/> + <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)"/> + <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)"/> + <expand macro="mapq_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> - <expand macro="pdf_output_data" filename="output.saturation.pdf" /> + <expand macro="pdf_output_data" filename="output.saturation.pdf"/> <data format="tabular" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string}: RPKM"/> <data format="tabular" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string}: raw count"/> - <expand macro="rscript_output_data" filename="output.saturation.r" /> + <expand macro="rscript_output_data" filename="output.saturation.r"/> </outputs> - <tests> - <test> + <test expect_num_outputs="4"> <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/> <param name="refgene" value="hg19.HouseKeepingGenes_30.bed"/> - <param name="rscript_output" value="true" /> + <param name="rscript_output" value="true"/> <output name="outputxls"> - <assert_contents> - <has_n_columns n="26" /> - <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" /> - </assert_contents> + <assert_contents> + <has_n_columns n="26"/> + <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*"/> + </assert_contents> </output> <output name="outputrawxls"> - <assert_contents> - <has_n_columns n="26" /> - <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" /> - </assert_contents> + <assert_contents> + <has_n_columns n="26"/> + <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*"/> + </assert_contents> </output> <output name="outputr"> - <assert_contents> - <has_text text="pdf('output.saturation.pdf')" /> - <has_line_matching expression="S5=c\(\d+\.\d+\)" /> - </assert_contents> + <assert_contents> + <has_text text="pdf('output.saturation.pdf')"/> + <has_line_matching expression="S5=c\(\d+\.\d+\)"/> + </assert_contents> </output> - <output name="outputpdf" file="output.saturation.pdf" compare="sim_size" /> + <output name="outputpdf" file="output.saturation.pdf" compare="sim_size"/> </test> </tests> - <help><![CDATA[ RPKM_saturation.py ++++++++++++++++++ @@ -163,7 +155,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>