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comparison callntvar.xml @ 5:b69e898b8109 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
author nml
date Fri, 24 Aug 2018 16:50:28 -0400
parents 8cdffc02d2e2
children dcd43b402eb3
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4:8cdffc02d2e2 5:b69e898b8109
1 <tool id="callntvar" name="Nucleotide Variants" version="0.1.0"> 1 <tool id="callntvar" name="Nucleotide Variants" version="0.4.2">
2 <description>Identifies nucleotide variants</description> 2 <description>Identifies nucleotide variants</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.3.1">quasitools</requirement> 4 <requirement type="package" version="0.4.2">quasitools</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 7
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
9 quasitools call ntvar $input_bam $ref_file 9 quasitools call ntvar $input_bam $ref_file
10 10
11 #if $error_rate: 11 #if $error_rate:
12 -e $error_rate 12 -e $error_rate
13 #end if 13 #end if
14 14
15 -o output.vcf 15 -o output.vcf
16 16
17 ]]></command> 17 ]]></command>
34 </assert_contents> 34 </assert_contents>
35 </output> 35 </output>
36 </test> 36 </test>
37 </tests> 37 </tests>
38 <help><![CDATA[ 38 <help><![CDATA[
39 39
40 Nucleotide Variants 40 Nucleotide Variants
41 =================== 41 ===================
42 42
43 Call nucleotide variants for a given BAM file and a supplied reference file. 43 Call nucleotide variants for a given BAM file and a supplied reference file.
44 44