Mercurial > repos > nml > quasitools
comparison callcodonvar.xml @ 5:b69e898b8109 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
author | nml |
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date | Fri, 24 Aug 2018 16:50:28 -0400 |
parents | 8cdffc02d2e2 |
children | dcd43b402eb3 |
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4:8cdffc02d2e2 | 5:b69e898b8109 |
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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> |