Mercurial > repos > nml > quasitools
comparison drmutations.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 |
comparison
equal
deleted
inserted
replaced
| 4:8cdffc02d2e2 | 5:b69e898b8109 |
|---|---|
| 1 <tool id="drmutations" name="Drug Resistance Mutations" version="0.1.0"> | 1 <tool id="drmutations" name="Drug Resistance Mutations" version="0.4.2"> |
| 2 <description></description> | 2 <description></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 drmutations $input_bam $ref_file $var_file $input_genes | 9 quasitools drmutations $input_bam $ref_file $var_file $input_genes |
| 10 | 10 |
| 11 #if $mutation_db: | 11 #if $mutation_db: |
| 12 $mutation_db | 12 $mutation_db |
| 13 #end if | 13 #end if |
| 14 | 14 |
| 15 #if $min_freq: | 15 #if $min_freq: |
| 16 -f $min_freq | 16 -f $min_freq |
| 17 #end if | 17 #end if |
| 18 | 18 |
| 19 #if $reporting_thres: | 19 #if $reporting_thres: |
| 20 -t $reporting_thres | 20 -t $reporting_thres |
| 21 #end if | 21 #end if |
| 22 | 22 |
| 23 -o output.csv | 23 -o output.csv |
| 24 | 24 |
| 25 ]]></command> | 25 ]]></command> |
| 26 <inputs> | 26 <inputs> |
| 27 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> | 27 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> |
| 28 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> | 28 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> |
| 29 <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" /> | 29 <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" /> |