Mercurial > repos > nilesh > rseqc
comparison geneBody_coverage.xml @ 59:dbedfc5f5a3c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
author | iuc |
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date | Sat, 18 Dec 2021 19:41:19 +0000 |
parents | f437057e46f1 |
children | 1421603cc95b |
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58:1a052c827e88 | 59:dbedfc5f5a3c |
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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 |