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comparison hydra.xml @ 1:1abf6b32ecfd draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f
author nml
date Wed, 13 Dec 2017 10:28:31 -0500
parents 71976cfc9022
children a7093d5933a8
comparison
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0:71976cfc9022 1:1abf6b32ecfd
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.2">quasitools</requirement> 4 <requirement type="package" version="0.2.2">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 '$forward' 8 quasitools hydra
9 9
10 #if $reverse: 10 ## Preparing file input.
11 '$reverse' 11 #if $data_type.type == "paired":
12
13 '$data_type.fastq_input1'
14 '$data_type.fastq_input2'
15
16 #elif $data_type.type == "collection":
17
18 '$data_type.fastq_input1.forward'
19 '$data_type.fastq_input1.reverse'
20
21 #elif $data_type.type == "single":
22
23 '$data_type.fastq_input1'
24
12 #end if 25 #end if
13 26
14 #if $mutation_db: 27 #if $mutation_db:
15 -m '$mutation_db' 28 -m '$mutation_db'
16 #end if 29 #end if
61 74
62 -o output 75 -o output
63 76
64 ]]></command> 77 ]]></command>
65 <inputs> 78 <inputs>
66 <param name="forward" type="data" format="fastq" optional="false" label="Forward read" /> 79 <conditional name="data_type">
67 <param name="reverse" type="data" format="fastq" optional="true" label="Reverse read" help="Not required."/> 80 <param name="type" type="select" label="Specify the read type.">
81 <option value="single">Single-end Data</option>
82 <option value="paired">Paired-end Data</option>
83 <option value="collection">Collection Paired-end Data</option>
84 </param>
85 <when value="single">
86 <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/>
87 </when>
88 <when value="paired">
89 <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/>
90 <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/>
91 </when>
92 <when value="collection">
93 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" />
94 </when>
95 </conditional>
68 <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." />
69 <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." />
70 <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="Reporting threshold" help="Minimum mutation frequency to report. Defaults to 20." />
71 <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." />
72 <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." />
88 <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" />
89 <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" />
90 </outputs> 118 </outputs>
91 <tests> 119 <tests>
92 <test> 120 <test>
93 <param name="forward" value="forward.fastq" /> 121 <param name="type" value="single"/>
122 <param name="fastq_input1" value="forward.fastq" />
94 <output name="output_coverage"> 123 <output name="output_coverage">
95 <assert_contents> 124 <assert_contents>
96 <has_text text="frame: 0" /> 125 <has_text text="frame: 0" />
97 <has_text text="1,0" /> 126 <has_text text="1,0" />
98 <has_text text="948,0" /> 127 <has_text text="948,0" />