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comparison srst2v2.xml @ 1:43cc60256036 draft

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author estrain
date Sat, 18 May 2019 19:09:56 -0400
parents efc202baae1f
children 6787d952242e
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0:efc202baae1f 1:43cc60256036
1 <tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0"> 1 <tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.3">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.2.0">srst2</requirement> 3 <requirement type="package" version="0.2.3">srst2</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 #if $paired_conditional.sPaired == "paired" 6 #if $paired_conditional.sPaired == "paired"
7 ln -s $paired_conditional.fastq1 sample_1.fastq; 7 ln -s $paired_conditional.fastq1 sample_1.fastq;
8 ln -s $paired_conditional.fastq2 sample_2.fastq; 8 ln -s $paired_conditional.fastq2 sample_2.fastq;
74 <param name="sPaired" type="select" label="Single-End or Paired-End FASTQ?"> 74 <param name="sPaired" type="select" label="Single-End or Paired-End FASTQ?">
75 <option value="single">Single-end</option> 75 <option value="single">Single-end</option>
76 <option value="paired">Paired-end</option> 76 <option value="paired">Paired-end</option>
77 </param> 77 </param>
78 <when value="single"> 78 <when value="single">
79 <param name="fastq1" type="data" format="fastq" label="FASTQ file" help="FASTQ" /> 79 <param name="fastq1" type="data" format="fastq,fastqsanger" label="FASTQ file" help="FASTQ" />
80 </when> 80 </when>
81 <when value="paired"> 81 <when value="paired">
82 <param name="fastq1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ" /> 82 <param name="fastq1" type="data" format="fastq,fastqsanger" label="Forward FASTQ file" help="FASTQ" />
83 <param name="fastq2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ" /> 83 <param name="fastq2" type="data" format="fastq,fastqsanger" label="Reverse FASTQ file" help="FASTQ" />
84 </when> 84 </when>
85 </conditional> 85 </conditional>
86 86
87 <conditional name="job_type"> 87 <conditional name="job_type">
88 <param name="job" type="select" label="MLST or Gene Presence/Absence?"> 88 <param name="job" type="select" label="MLST or Gene Presence/Absence?">
89 <option value="none">none</option>
89 <option value="mlst">MLST</option> 90 <option value="mlst">MLST</option>
90 <option value="gene">Gene</option> 91 <option value="gene">Gene</option>
91 </param> 92 </param>
92 <when value="mlst"> 93 <when value="mlst">
93 <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" /> 94 <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />