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comparison consensus.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="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>