Mercurial > repos > nml > quasitools
diff hydra.xml @ 2:a7093d5933a8 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit de4309426401ce655435d6867b05c3673b9d086f
author | nml |
---|---|
date | Mon, 26 Mar 2018 14:23:30 -0400 |
parents | 1abf6b32ecfd |
children | 8cdffc02d2e2 |
line wrap: on
line diff
--- a/hydra.xml Wed Dec 13 10:28:31 2017 -0500 +++ b/hydra.xml Mon Mar 26 14:23:30 2018 -0400 @@ -1,7 +1,7 @@ <tool id="hydra" name="Hydra pipeline" version="0.1.0"> <description>Identifies drug resistance within an NGS dataset</description> <requirements> - <requirement type="package" version="0.2.2">quasitools</requirement> + <requirement type="package" version="0.2.3">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -95,7 +95,7 @@ </conditional> <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." /> <param name="reporting_threshold" type="integer" optional="true" min="1" max="100" value="1" label="Reporting threshold. Defaults to 1." help="Minimum mutation frequency to report." /> - <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Reporting threshold" help="Minimum mutation frequency to report. Defaults to 20." /> + <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Consensus percentage" help="Minimum mutation frequency to report. Defaults to 20." /> <param name="length_cutoff" type="integer" optional="true" min="0" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." /> <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose average quality score is less than the specified score will be filtered out. Defaults to 30." /> <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021."/> @@ -115,6 +115,9 @@ <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" /> <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" /> <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" /> + <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta"> + <filter>generate_consensus</filter> + </data> </outputs> <tests> <test>