Mercurial > repos > nilesh > rseqc

comparison junction_saturation.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 5873cd7afb67
children 1421603cc95b
comparison
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58:1a052c827e88 59:dbedfc5f5a3c
1 <tool id="rseqc_junction_saturation" name="Junction Saturation" version="@WRAPPER_VERSION@.1"> 1 <tool id="rseqc_junction_saturation" name="Junction Saturation" version="@TOOL_VERSION@.1">
2 <description>detects splice junctions from each subset and compares them to reference gene model</description> 2 <description>detects splice junctions from each subset and compares them to reference gene model</description>
3 3 <expand macro="bio_tools"/>
4 <macros> 4 <macros>
5 <import>rseqc_macros.xml</import> 5 <import>rseqc_macros.xml</import>
6 </macros> 6 </macros>
7 7
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
60 </outputs> 60 </outputs>
61 61
62 <tests> 62 <tests>
63 <test> 63 <test>
64 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 64 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
65 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> 65 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
66 <param name="rscript_output" value="true" /> 66 <param name="rscript_output" value="true" />
67 <output name="outputr" file="output.junctionSaturation_plot.r" compare="sim_size"> 67 <output name="outputr" file="output.junctionSaturation_plot_r" compare="sim_size">
68 <assert_contents> 68 <assert_contents>
69 <has_line line="pdf('output.junctionSaturation_plot.pdf')" /> 69 <has_line line="pdf('output.junctionSaturation_plot.pdf')" />
70 <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)" /> 70 <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)" />
71 </assert_contents> 71 </assert_contents>
72 </output> 72 </output>