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comparison consensus.xml @ 9:18aad692772a draft default tip

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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:06:36 +0000
parents 9def47f3c1e4
children
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8:9def47f3c1e4 9:18aad692772a
1 <tool id="consensus" name="Consensus Sequence" version="0.7.0"> 1 <tool id="consensus" name="Consensus Sequence" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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 <macros>
4 <requirement type="package" version="0.7.0">quasitools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"/>
6 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
7 8
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 9 ln -s $input_bam '${input_bam.name}' &&
9 quasitools consensus $input_bam $ref_file 10 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
11
12 quasitools consensus '${input_bam.name}' $ref_file
10 13
11 #if $fasta_id.type == 'default': 14 #if $fasta_id.type == 'default':
12 -i '${input_bam.element_identifier}' 15 -i '${input_bam.element_identifier}'
13 #elif $fasta_id.type == 'custom': 16 #elif $fasta_id.type == 'custom':
14 -i '${fasta_id.custom_id}' 17 -i '${fasta_id.custom_id}'
86 When percentage is set to 100, the most frequent base will be incorporated (note: in the case of a tie the base will be chosen in reverse alphabetical order). Insertions that are at least a multiple of 3 will be incorporated (i.e. codon length). 89 When percentage is set to 100, the most frequent base will be incorporated (note: in the case of a tie the base will be chosen in reverse alphabetical order). Insertions that are at least a multiple of 3 will be incorporated (i.e. codon length).
87 When percentage is less than 100, the base that has frequency greater than equal to percentage set will be incorporated, tie breaking same as above. 90 When percentage is less than 100, the base that has frequency greater than equal to percentage set will be incorporated, tie breaking same as above.
88 When there is zero coverage or no bases meet the percentage threshold (only when percentage is < 100) a n will be incorporated. 91 When there is zero coverage or no bases meet the percentage threshold (only when percentage is < 100) a n will be incorporated.
89 92
90 ]]></help> 93 ]]></help>
91 <citations> 94 <expand macro="citations" />
92 <citation type="bibtex">
93 @misc{GitHubquasitoolsconsensus,
94 title = {quasitools consensus},
95 publisher = {phac-nml},
96 journal = {GitHub repository},
97 url = {https://github.com/phac-nml/quasitools},
98 }
99 </citation>
100 </citations>
101 </tool> 95 </tool>