Mercurial > repos > nml > quasitools
comparison consensus.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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| 4:8cdffc02d2e2 | 5:b69e898b8109 |
|---|---|
| 1 <tool id="consensus" name="Consensus Sequence" version="0.2.0"> | 1 <tool id="consensus" name="Consensus Sequence" version="0.4.2"> |
| 2 <description>Generate a consensus sequence from a BAM file</description> | 2 <description>Generate a consensus sequence from a BAM file</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 consensus $input_bam $ref_file | 9 quasitools consensus $input_bam $ref_file |
| 10 | 10 |
| 11 #if $fasta_id.type == 'default': | 11 #if $fasta_id.type == 'default': |
| 12 -i '${input_bam.element_identifier}' | 12 -i '${input_bam.element_identifier}' |
| 13 #elif $fasta_id.type == 'custom': | 13 #elif $fasta_id.type == 'custom': |
| 14 -i '${fasta_id.custom_id}' | 14 -i '${fasta_id.custom_id}' |
| 15 #end if | 15 #end if |
| 16 | 16 |
| 17 #if $base_type.type == 'mixed': | 17 #if $base_type.type == 'mixed': |
| 18 -p $base_type.percentage | 18 -p $base_type.percentage |
| 19 #end if | 19 #end if |
| 20 | 20 |
| 21 -o output.fasta | 21 -o output.fasta |
| 22 | 22 |
| 23 ]]></command> | 23 ]]></command> |