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comparison tin.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
comparison
equal deleted inserted replaced
59:dbedfc5f5a3c 60:1421603cc95b
1 <tool id="rseqc_tin" name="Transcript Integrity Number" version="@TOOL_VERSION@.1"> 1 <tool id="rseqc_tin" name="Transcript Integrity Number" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description> 2 <description>
3 evaluates RNA integrity at a transcript level 3 evaluates RNA integrity at a transcript level
4 </description> 4 </description>
5 <expand macro="bio_tools"/> 5 <expand macro="bio_tools"/>
6 <macros> 6 <macros>
15 15
16 <!-- Generate output files here because tin.py removes all instances of "bam" 16 <!-- Generate output files here because tin.py removes all instances of "bam"
17 in the filename --> 17 in the filename -->
18 <command><![CDATA[ 18 <command><![CDATA[
19 #import re 19 #import re
20 ln -sf '${input}' 'input.bam' && 20 #set $input_list = []
21 ln -sf '${input.metadata.bam_index}' 'input.bam.bai' && 21 #for $i, $input in enumerate($input):
22 tin.py -i 'input.bam' --refgene='${refgene}' --minCov=${minCov} 22 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
23 #if $safename in $input_list:
24 #set $safename = str($safename) + "." + str($i)
25 #end if
26 $input_list.append($safename)
27 ln -sf '${input}' '${safename}.bam' &&
28 ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' &&
29 echo '${safename}.bam' >> 'input_list.txt' &&
30 #end for
31 tin.py -i 'input_list.txt' --refgene='${refgene}' --minCov=${minCov}
23 --sample-size=${samplesize} ${subtractbackground} 32 --sample-size=${samplesize} ${subtractbackground}
33 && mv *summary.txt summary.tab
34 && mv *tin.xls tin.xls
24 ]]> 35 ]]>
25 </command> 36 </command>
26 37
27 <inputs> 38 <inputs>
28 <expand macro="bam_param" /> 39 <param name="input" type="data" format="bam" multiple="true" label="Input BAM file" help="(--input-file)"/>
29 <expand macro="refgene_param" /> 40 <expand macro="refgene_param" />
30 <param name="minCov" type="integer" value="10" label="Minimum coverage (default=10)" 41 <param name="minCov" type="integer" value="10" label="Minimum coverage (default=10)"
31 help="Minimum number of reads mapped to a transcript (--minCov)." /> 42 help="Minimum number of reads mapped to a transcript (--minCov)." />
32 <param name="samplesize" type="integer" value="100" label="Sample size (default=100)" 43 <param name="samplesize" type="integer" value="100" label="Sample size (default=100)"
33 help="Number of equal-spaced nucleotide positions picked from mRNA. 44 help="Number of equal-spaced nucleotide positions picked from mRNA.
39 intronic reads). Only use this option if there are substantial 50 intronic reads). Only use this option if there are substantial
40 intronic reads (--subtract-background)." /> 51 intronic reads (--subtract-background)." />
41 </inputs> 52 </inputs>
42 53
43 <outputs> 54 <outputs>
44 <data name="outputsummary" format="tabular" from_work_dir="input.summary.txt" label="TIN on ${on_string} (summary)" /> 55 <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)" />
45 <data name="outputxls" format="xls" from_work_dir="input.tin.xls" label="TIN on ${on_string} (tin)" /> 56 <data name="outputxls" format="xls" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" />
46 </outputs> 57 </outputs>
47 58
48 <!-- PDF Files contain R version, must avoid checking for diff --> 59 <!-- PDF Files contain R version, must avoid checking for diff -->
49 <tests> 60 <tests>
50 <test> 61 <test expect_num_outputs="2">
51 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 62 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
52 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 63 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
53 <output name="outputsummary"> 64 <output name="outputsummary" file="summary.tin.txt" ftype="tabular"/>
54 <assert_contents> 65 <output name="outputxls" file="output.tin.xls" ftype="xls"/>
55 <has_line_matching expression="^Bam_file\tTIN\(mean\)\tTIN\(median\)\tTIN\(stdev\)$" />
56 <has_line_matching expression="^input\.bam\t8\.8709677419\d+\t8\.8709677419\d+\t0\.0$" />
57 </assert_contents>
58 </output>
59 <output name="outputxls" file="output.tin.xls"/>
60 </test> 66 </test>
61 </tests> 67 </tests>
62 68
63 <help><![CDATA[ 69 <help><![CDATA[
64 ## tin.py 70 ## tin.py