Mercurial > repos > nml > quasitools
comparison hydra.xml @ 4:8cdffc02d2e2 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit 19e0f266ee455b82432e2d7b987b35de8c7a14d5
author | nml |
---|---|
date | Wed, 25 Apr 2018 10:38:00 -0400 |
parents | a7093d5933a8 |
children | b69e898b8109 |
comparison
equal
deleted
inserted
replaced
3:8dacd75ca8f1 | 4:8cdffc02d2e2 |
---|---|
1 <tool id="hydra" name="Hydra pipeline" version="0.1.0"> | 1 <tool id="hydra" name="Hydra pipeline" version="0.2.0"> |
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="0.2.3">quasitools</requirement> | 4 <requirement type="package" version="0.3.1">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 |
62 | 62 |
63 #if $min_freq: | 63 #if $min_freq: |
64 -mf '$min_freq' | 64 -mf '$min_freq' |
65 #end if | 65 #end if |
66 | 66 |
67 #if $generate_consensus: | 67 #if $consensus.consensus_bool == "true_consensus": |
68 --generate_consensus | 68 --generate_consensus |
69 | |
70 #if $consensus.fasta_id.type == "default": | |
71 --id | |
72 #if $data_type.type == "paired": | |
73 '${fastq_input1.element_identifier}'_'${fastq_input2.element_identifier}' | |
74 #elif $data_type.type == "single": | |
75 '${fastq_input1.element_identifier}' | |
76 #end if | |
77 #elif $consensus.fasta_id.type == "custom": | |
78 --id '$consensus.fasta_id.custom_id' | |
79 #end if | |
69 #end if | 80 #end if |
70 | 81 |
71 #if $filter_ns: | 82 #if $filter_ns: |
72 --ns | 83 --ns |
73 #end if | 84 #end if |
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."/> | 112 <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." /> | 113 <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." /> | 114 <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." /> |
104 <param name="min_ac" type="integer" optional="true" min="0" max="5000" label="Minimum allele count" value="5" help="Minimum required allele count for variant to be considered later on in the pipeline. Defaults to 5." /> | 115 <param name="min_ac" type="integer" optional="true" min="0" max="5000" label="Minimum allele count" value="5" help="Minimum required allele count for variant to be considered later on in the pipeline. Defaults to 5." /> |
105 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="Minimum required frequency for variant to be considered later on in the pipeline. Defaults to 0.01." /> | 116 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="Minimum required frequency for variant to be considered later on in the pipeline. Defaults to 0.01." /> |
106 <param name="generate_consensus" type="boolean" truevalue="--generate_consensus" falsevalue="" checked="False" label="Generate consensus" /> | 117 <conditional name="consensus"> |
118 <param name="consensus_bool" type="select" label="Generate consensus sequence." multiple="false" display="radio"> | |
119 <option value="true_consensus">True</option> | |
120 <option selected="true" value="false_consensus">False</option> | |
121 </param> | |
122 <when value="true_consensus"> | |
123 <conditional name="fasta_id"> | |
124 <param name="type" type="select" label="Specify consensus fasta identifier" multiple="false" display="radio"> | |
125 <option value="default" >Use fasta dataset name</option> | |
126 <option value="custom">Use custom name</option> | |
127 </param> | |
128 <when value="default"> | |
129 </when> | |
130 <when value="custom"> | |
131 <param name="custom_id" type="text" optional="false" value="custom_id" label="Fasta identifier" help="Type in a fasta identifier."/> | |
132 </when> | |
133 </conditional> | |
134 </when> | |
135 <when value="false_consensus"> | |
136 </when> | |
137 </conditional> | |
107 <param name="filter_ns" type="boolean" truevalue="--ns" falsevalue="" checked="False" label="Filter out n's" /> | 138 <param name="filter_ns" type="boolean" truevalue="--ns" falsevalue="" checked="False" label="Filter out n's" /> |
108 </inputs> | 139 </inputs> |
109 <outputs> | 140 <outputs> |
110 <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" /> | 141 <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" /> |
111 <data format="bam" label="HyDRA: bam.bai output" name="output_bam_bai" from_work_dir="output/align.bam.bai" /> | 142 <data format="bam" label="HyDRA: bam.bai output" name="output_bam_bai" from_work_dir="output/align.bam.bai" /> |
113 <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" /> | 144 <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" /> | 145 <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" /> | 146 <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" /> | 147 <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" /> | 148 <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"> | 149 <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta" > |
119 <filter>generate_consensus</filter> | 150 <filter>consensus['consensus_bool'] == "true_consensus"</filter> |
120 </data> | 151 </data> |
121 </outputs> | 152 </outputs> |
122 <tests> | 153 <tests> |
123 <test> | 154 <test> |
124 <param name="type" value="single"/> | 155 <param name="type" value="single"/> |