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comparison callcodonvar.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
comparison
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4:8cdffc02d2e2 5:b69e898b8109
1 <tool id="callcodonvar" name="Codon Variants" version="0.1.0"> 1 <tool id="callcodonvar" name="Codon Variants" version="0.4.2">
2 <description>Identifies codon variants and non-synonymous/synonymous mutations</description> 2 <description>Identifies codon variants and non-synonymous/synonymous mutations</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 cat $input_genes && 8 cat $input_genes &&
9 9
10 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 10 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
11 quasitools call codonvar $input_bam $ref_file $offset $input_genes 11 quasitools call codonvar $input_bam $ref_file $offset $input_genes
12 12
13 #if $error_rate: 13 #if $error_rate:
14 -e $error_rate 14 -e $error_rate
15 #end if 15 #end if
16 16
17 -o output.csv 17 -o output.csv
18 18
19 ]]></command> 19 ]]></command>
44 <help><![CDATA[ 44 <help><![CDATA[
45 45
46 Codon Variants 46 Codon Variants
47 ============== 47 ==============
48 48
49 Call codon variants for a given BAM. A report is generated that details nucleotide variants within a 49 Call codon variants for a given BAM. A report is generated that details nucleotide variants within a
50 codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to 50 codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to
51 a synonymous or non-synonymous mutation. 51 a synonymous or non-synonymous mutation.
52 52
53 ]]></help> 53 ]]></help>
54 <citations> 54 <citations>