Mercurial > repos > nml > quasitools
comparison 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 |
comparison
equal
deleted
inserted
replaced
1:1abf6b32ecfd | 2:a7093d5933a8 |
---|---|
1 <tool id="hydra" name="Hydra pipeline" version="0.1.0"> | 1 <tool id="hydra" name="Hydra pipeline" version="0.1.0"> |
2 <description>Identifies drug resistance within an NGS dataset</description> | 2 <description>Identifies drug resistance within an NGS dataset</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.2.2">quasitools</requirement> | 4 <requirement type="package" version="0.2.3">quasitools</requirement> |
5 </requirements> | 5 </requirements> |
6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
7 | 7 |
8 quasitools hydra | 8 quasitools hydra |
9 | 9 |
93 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" /> | 93 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" /> |
94 </when> | 94 </when> |
95 </conditional> | 95 </conditional> |
96 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." /> | 96 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." /> |
97 <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." /> | 97 <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." /> |
98 <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." /> | 98 <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." /> |
99 <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." /> | 99 <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." /> |
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." /> | 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." /> |
101 <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."/> | 101 <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."/> |
102 <param name="min_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for variant to be considered later on in the pipeline. Defaults to 30." /> | 102 <param name="min_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for variant to be considered later on in the pipeline. Defaults to 30." /> |
103 <param name="min_depth" type="integer" optional="true" min="0" max="5000" label="Minimum depth" value="100" help="Minimum required depth for variant to be considered later on in the pipeline. Defaults to 100." /> | 103 <param name="min_depth" type="integer" optional="true" min="0" max="5000" label="Minimum depth" value="100" help="Minimum required depth for variant to be considered later on in the pipeline. Defaults to 100." /> |
113 <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" /> | 113 <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" /> |
114 <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" /> | 114 <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" /> |
115 <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" /> | 115 <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" /> |
116 <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" /> | 116 <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" /> |
117 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" /> | 117 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" /> |
118 <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta"> | |
119 <filter>generate_consensus</filter> | |
120 </data> | |
118 </outputs> | 121 </outputs> |
119 <tests> | 122 <tests> |
120 <test> | 123 <test> |
121 <param name="type" value="single"/> | 124 <param name="type" value="single"/> |
122 <param name="fastq_input1" value="forward.fastq" /> | 125 <param name="fastq_input1" value="forward.fastq" /> |