Mercurial > repos > nilesh > rseqc
diff junction_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 | 5968573462fa |
| children |
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--- a/junction_saturation.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/junction_saturation.xml Tue Apr 09 11:24:55 2024 +0000 @@ -4,8 +4,8 @@ <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[junction_saturation.py --version]]></version_command> <command><![CDATA[ @BAM_SAM_INPUTS@ @@ -23,13 +23,12 @@ #end if ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="refgene_param" /> - <expand macro="min_intron_param" /> - <param name="min_coverage" type="integer" label="Minimum number of supporting reads to call a junction (default=1)" value="1" help="(--min-coverage)" /> - <expand macro="mapq_param" /> + <expand macro="bam_sam_param"/> + <expand macro="refgene_param"/> + <expand macro="min_intron_param"/> + <param name="min_coverage" type="integer" label="Minimum number of supporting reads to call a junction (default=1)" value="1" help="(--min-coverage)"/> + <expand macro="mapq_param"/> <conditional name="percentiles_type"> <param name="percentiles_type_selector" type="select" label="Sampling bounds and frequency"> <option value="default" selected="true">Default sampling bounds and frequency</option> @@ -37,40 +36,37 @@ </param> <when value="specify"> <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" help="(--percentile-floor)"> - <validator type="in_range" min="0" max="100" /> + <validator type="in_range" min="0" max="100"/> </param> <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" help="(--percentile-ceiling)"> - <validator type="in_range" min="0" max="100" /> + <validator type="in_range" min="0" max="100"/> </param> <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" help="(--percentile-step)"> - <validator type="in_range" min="0" max="100" /> + <validator type="in_range" min="0" max="100"/> </param> </when> <when value="default"/> </conditional> - <expand macro="rscript_output_param" /> + <expand macro="rscript_output_param"/> </inputs> - <outputs> <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string}: junction saturation (PDF)"/> <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string}: junction saturation (Rscript)"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> + <test expect_num_outputs="2"> + <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="outputr" file="output.junctionSaturation_plot_r" compare="sim_size"> <assert_contents> - <has_line line="pdf('output.junctionSaturation_plot.pdf')" /> - <has_line line="x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100)" /> + <has_line line="pdf('output.junctionSaturation_plot.pdf')"/> + <has_line line="x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100)"/> </assert_contents> </output> - <output name="outputpdf" file="output.junctionSaturation_plot.pdf" compare="sim_size" /> + <output name="outputpdf" file="output.junctionSaturation_plot.pdf" compare="sim_size"/> </test> </tests> - <help><![CDATA[ junction_saturation.py ++++++++++++++++++++++ @@ -120,7 +116,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>