Mercurial > repos > nml > quasitools
diff callcodonvar.xml @ 5:b69e898b8109 draft
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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--- a/callcodonvar.xml Wed Apr 25 10:38:00 2018 -0400 +++ b/callcodonvar.xml Fri Aug 24 16:50:28 2018 -0400 @@ -1,17 +1,17 @@ -<tool id="callcodonvar" name="Codon Variants" version="0.1.0"> +<tool id="callcodonvar" name="Codon Variants" version="0.4.2"> <description>Identifies codon variants and non-synonymous/synonymous mutations</description> <requirements> - <requirement type="package" version="0.3.1">quasitools</requirement> + <requirement type="package" version="0.4.2">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - cat $input_genes && + cat $input_genes && ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && - quasitools call codonvar $input_bam $ref_file $offset $input_genes + quasitools call codonvar $input_bam $ref_file $offset $input_genes #if $error_rate: - -e $error_rate + -e $error_rate #end if -o output.csv @@ -46,7 +46,7 @@ Codon Variants ============== -Call codon variants for a given BAM. A report is generated that details nucleotide variants within a +Call codon variants for a given BAM. A report is generated that details nucleotide variants within a codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to a synonymous or non-synonymous mutation.