Mercurial > repos > nilesh > rseqc

comparison RNA_fragment_size.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_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@.1"> 1 <tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@.1">
2 <description> 2 <description>
3 calculates the fragment size for each gene/transcript 3 calculates the fragment size for each gene/transcript
4 </description> 4 </description>
5 5 <expand macro="bio_tools"/>
6 <macros> 6 <macros>
7 <import>rseqc_macros.xml</import> 7 <import>rseqc_macros.xml</import>
8 </macros> 8 </macros>
9 9
10 <expand macro="requirements" /> 10 <expand macro="requirements" />
32 </outputs> 32 </outputs>
33 33
34 <tests> 34 <tests>
35 <test> 35 <test>
36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
37 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> 37 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
38 <output name="output"> 38 <output name="output">
39 <assert_contents> 39 <assert_contents>
40 <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$" /> 40 <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$" />
41 <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$" /> 41 <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$" />
42 <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$" /> 42 <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$" />