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comparison RNA_fragment_size.xml @ 54:5873cd7afb67 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 62a9135bf04aec398d3172d17ccd60f5242d8e82
author iuc
date Wed, 13 Jun 2018 18:02:25 -0400
parents 09846d5169fa
children dbedfc5f5a3c
comparison
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53:080fd5739bb4 54:5873cd7afb67
1 <tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@"> 1 <tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_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
6 <macros> 6 <macros>
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" />
38 <output name="output" file="output.RNA_fragment_size.txt" /> 38 <output name="output">
39 <assert_contents>
40 <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$" />
41 <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$" />
42 <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$" />
43 <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$" />
44 <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$" />
45 <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$" />
46 <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$" />
47 <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$" />
48 </assert_contents>
49 </output>
39 </test> 50 </test>
40 </tests> 51 </tests>
41 52
42 <help><![CDATA[ 53 <help><![CDATA[
43 RNA_fragment_size.py 54 RNA_fragment_size.py