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comparison consensus.xml @ 7:dcd43b402eb3 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
author nml
date Fri, 23 Nov 2018 15:43:16 -0500
parents b69e898b8109
children 9def47f3c1e4
comparison
equal deleted inserted replaced
6:9fb9fed71486 7:dcd43b402eb3
1 <tool id="consensus" name="Consensus Sequence" version="0.4.2"> 1 <tool id="consensus" name="Consensus Sequence" version="0.5.1">
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="0.4.2">quasitools</requirement> 4 <requirement type="package" version="0.5.1">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
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. 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.
88 When there is zero coverage or no bases meet the percentage threshold (only when percentage is < 100) a n will be incorporated. 88 When there is zero coverage or no bases meet the percentage threshold (only when percentage is < 100) a n will be incorporated.
89 89
90 ]]></help> 90 ]]></help>
91 <citations> 91 <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>
92 </citations> 100 </citations>
93 </tool> 101 </tool>