Mercurial > repos > nilesh > rseqc

comparison geneBody_coverage.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 f437057e46f1
children 1421603cc95b
comparison
equal deleted inserted replaced
58:1a052c827e88 59:dbedfc5f5a3c
1 <tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.3"> 1 <tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@TOOL_VERSION@.3">
2 <description> 2 <description>Read coverage over gene body</description>
3 Read coverage over gene body. 3 <expand macro="bio_tools"/>
4 </description> 4 <macros>
5 5 <import>rseqc_macros.xml</import>
6 <macros> 6 </macros>
7 <import>rseqc_macros.xml</import>
8 </macros>
9
10 <expand macro="requirements" /> 7 <expand macro="requirements" />
11 8 <expand macro="stdio" />
12 <expand macro="stdio" /> 9 <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
13 10 <command><![CDATA[
14 <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
15
16 <command><![CDATA[
17 #if str($batch_mode.batch_mode_selector) == "merge": 11 #if str($batch_mode.batch_mode_selector) == "merge":
18 #import re 12 #import re
19 #set $input_list = [] 13 #set $input_list = []
20 #for $i, $input in enumerate($batch_mode.inputs): 14 #for $i, $input in enumerate($batch_mode.inputs):
21 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier) 15 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
72 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 66 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
73 </conditional> 67 </conditional>
74 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> 68 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
75 <param name="rscript_output" value="true" /> 69 <param name="rscript_output" value="true" />
76 <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size" /> 70 <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size" />
77 <output name="outputr" file="output.geneBodyCoverage.r" /> 71 <output name="outputr" file="output.geneBodyCoverage_r" />
78 <output name="outputtxt" file="output.geneBodyCoverage.txt" /> 72 <output name="outputtxt" file="output.geneBodyCoverage.txt" />
79 </test> 73 </test>
80 <test> 74 <test>
81 <conditional name="batch_mode"> 75 <conditional name="batch_mode">
82 <param name="batch_mode_selector" value="merge" /> 76 <param name="batch_mode_selector" value="merge" />
83 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 77 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
84 </conditional> 78 </conditional>
85 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> 79 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
86 <param name="rscript_output" value="true" /> 80 <param name="rscript_output" value="true" />
87 <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size" /> 81 <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size" />
88 <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf" compare="sim_size" /> 82 <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf" compare="sim_size" />
89 <output name="outputr" file="output2.geneBodyCoverage.r" /> 83 <output name="outputr" file="output2.geneBodyCoverage_r" />
90 <output name="outputtxt" file="output2.geneBodyCoverage.txt" /> 84 <output name="outputtxt" file="output2.geneBodyCoverage.txt" />
91 </test> 85 </test>
92 86
93 </tests> 87 </tests>
94 88