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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 473382134e56
children
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62:473382134e56 63:27e16a30667a
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>rseqc_macros.xml</import> 6 <import>rseqc_macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="bio_tools"/> 8 <expand macro="bio_tools"/>
9 9 <expand macro="requirements"/>
10 <expand macro="requirements" /> 10 <expand macro="stdio"/>
11
12 <expand macro="stdio" />
13
14 <version_command><![CDATA[tin.py --version]]></version_command> 11 <version_command><![CDATA[tin.py --version]]></version_command>
15
16 <!-- Generate output files here because tin.py removes all instances of "bam" 12 <!-- Generate output files here because tin.py removes all instances of "bam"
17 in the filename --> 13 in the filename -->
18 <command><![CDATA[ 14 <command><![CDATA[
19 #import re 15 #import re
20 #set $input_list = [] 16 #set $input_list = []
32 --sample-size=${samplesize} ${subtractbackground} 28 --sample-size=${samplesize} ${subtractbackground}
33 && mv *summary.txt summary.tab 29 && mv *summary.txt summary.tab
34 && mv *tin.xls tin.xls 30 && mv *tin.xls tin.xls
35 ]]> 31 ]]>
36 </command> 32 </command>
37
38 <inputs> 33 <inputs>
39 <param name="input" type="data" format="bam" multiple="true" label="Input BAM file" help="(--input-file)"/> 34 <param name="input" type="data" format="bam" multiple="true" label="Input BAM file" help="(--input-file)"/>
40 <expand macro="refgene_param" /> 35 <expand macro="refgene_param"/>
41 <param name="minCov" type="integer" value="10" label="Minimum coverage (default=10)" 36 <param name="minCov" type="integer" value="10" label="Minimum coverage (default=10)" help="Minimum number of reads mapped to a transcript (--minCov)."/>
42 help="Minimum number of reads mapped to a transcript (--minCov)." /> 37 <param name="samplesize" type="integer" value="100" label="Sample size (default=100)" help="Number of equal-spaced nucleotide positions picked from mRNA. Note: if this number is larger than the length of mRNA (L), it will be halved until is's smaller than L. (--sample-size)."/>
43 <param name="samplesize" type="integer" value="100" label="Sample size (default=100)" 38 <param name="subtractbackground" type="boolean" value="false" falsevalue="" truevalue="--subtract-background" label="Subtract background noise (default=No)" help="Subtract background noise (estimated from intronic reads). Only use this option if there are substantial intronic reads (--subtract-background)."/>
44 help="Number of equal-spaced nucleotide positions picked from mRNA.
45 Note: if this number is larger than the length of mRNA (L), it will
46 be halved until is's smaller than L. (--sample-size)." />
47 <param name="subtractbackground" type="boolean" value="false" falsevalue=""
48 truevalue="--subtract-background" label="Subtract background noise
49 (default=No)" help="Subtract background noise (estimated from
50 intronic reads). Only use this option if there are substantial
51 intronic reads (--subtract-background)." />
52 </inputs> 39 </inputs>
53
54 <outputs> 40 <outputs>
55 <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)" /> 41 <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)"/>
56 <data name="outputxls" format="tabular" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" /> 42 <data name="outputxls" format="tabular" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)"/>
57 </outputs> 43 </outputs>
58
59 <!-- PDF Files contain R version, must avoid checking for diff --> 44 <!-- PDF Files contain R version, must avoid checking for diff -->
60 <tests> 45 <tests>
61 <test expect_num_outputs="2"> 46 <test expect_num_outputs="2">
62 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 47 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
63 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 48 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
64 <output name="outputsummary" file="summary.tin.txt" ftype="tabular"/> 49 <output name="outputsummary" file="summary.tin.txt" ftype="tabular"/>
65 <output name="outputxls" file="output.tin.xls" ftype="tabular"/> 50 <output name="outputxls" file="output.tin.xls" ftype="tabular"/>
66 </test> 51 </test>
67 </tests> 52 </tests>
68
69 <help><![CDATA[ 53 <help><![CDATA[
70 ## tin.py 54 ## tin.py
71 55
72 This program is designed to evaluate RNA integrity at transcript level. TIN 56 This program is designed to evaluate RNA integrity at transcript level. TIN
73 (transcript integrity number) is named in analogous to RIN (RNA integrity 57 (transcript integrity number) is named in analogous to RIN (RNA integrity
147 131
148 @ABOUT@ 132 @ABOUT@
149 133
150 ]]> 134 ]]>
151 </help> 135 </help>
152 136 <expand macro="citations"/>
153 <expand macro="citations" />
154
155 </tool> 137 </tool>