Mercurial > repos > estrain > srst2

comparison srst2v2.xml @ 2:6787d952242e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author estrain
date Sun, 19 May 2019 07:36:55 -0400
parents 43cc60256036
children 8bf4865cc3e3
comparison
equal deleted inserted replaced
1:43cc60256036 2:6787d952242e
1 <tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.3"> 1 <tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.2.3">srst2</requirement> 3 <requirement type="package" version="0.2.0">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;
9 #else if $paired_conditional.sPaired == "paired_coll"
10 ln -s $paired_conditional.coll.forward sample_1.fastq;
11 ln -s $paired_conditional.coll.reverse sample_2.fastq;
9 #end if 12 #end if
10 13
11 srst2 14 srst2
12 15
13 #if $paired_conditional.sPaired == "single" 16 #if $paired_conditional.sPaired == "single"
14 --input_se $paired_conditional.fastq1 17 --input_se $paired_conditional.fastq1
15 #else if $paired_conditional.sPaired == "paired" 18 #else if $paired_conditional.sPaired == "paired"
19 --input_pe sample_1.fastq sample_2.fastq
20 #else if $paired_conditional.sPaired == "paired_coll"
16 --input_pe sample_1.fastq sample_2.fastq 21 --input_pe sample_1.fastq sample_2.fastq
17 #end if 22 #end if
18 23
19 --output srst2out 24 --output srst2out
20 --save_scores 25 --save_scores
25 --mlst_delimiter $job_type.mlstdelim 30 --mlst_delimiter $job_type.mlstdelim
26 --mlst_max_mismatch $job_type.mlst_max_mismatch 31 --mlst_max_mismatch $job_type.mlst_max_mismatch
27 #else if $job_type.job == "gene" 32 #else if $job_type.job == "gene"
28 --gene_db $job_type.genedb 33 --gene_db $job_type.genedb
29 --gene_max_mismatch $job_type.gene_max_mismatch 34 --gene_max_mismatch $job_type.gene_max_mismatch
35 #else if $job_type.job == "nost"
36 --mlst_db $job_type.mlst_db
37 --mlst_delimiter $job_type.mlstdelim
38 --mlst_max_mismatch $job_type.mlst_max_mismatch
30 #end if 39 #end if
31 40
32 #if $options.select == "advanced" 41 #if $options.select == "advanced"
33 #if $options.min_coverage 42 #if $options.min_coverage
34 --min_coverage $options.min_coverage 43 --min_coverage $options.min_coverage
70 79
71 ]]></command> 80 ]]></command>
72 <inputs> 81 <inputs>
73 <conditional name="paired_conditional"> 82 <conditional name="paired_conditional">
74 <param name="sPaired" type="select" label="Single-End or Paired-End FASTQ?"> 83 <param name="sPaired" type="select" label="Single-End or Paired-End FASTQ?">
75 <option value="single">Single-end</option> 84 <option value="single">Single FASTQ</option>
76 <option value="paired">Paired-end</option> 85 <option value="paired">Forward and Reverse FASTQ</option>
86 <option value="paired_coll">Paired FASTQ Collection</option>
77 </param> 87 </param>
78 <when value="single"> 88 <when value="single">
79 <param name="fastq1" type="data" format="fastq,fastqsanger" label="FASTQ file" help="FASTQ" /> 89 <param name="fastq1" type="data" format="fastq,fastqsanger" label="FASTQ file" help="FASTQ" />
80 </when> 90 </when>
81 <when value="paired"> 91 <when value="paired">
82 <param name="fastq1" type="data" format="fastq,fastqsanger" label="Forward FASTQ file" help="FASTQ" /> 92 <param name="fastq1" type="data" format="fastq,fastqsanger" label="Forward FASTQ file" help="FASTQ" />
83 <param name="fastq2" type="data" format="fastq,fastqsanger" label="Reverse FASTQ file" help="FASTQ" /> 93 <param name="fastq2" type="data" format="fastq,fastqsanger" label="Reverse FASTQ file" help="FASTQ" />
84 </when> 94 </when>
95 <when value="paired_coll">
96 <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger" collection_type="paired" />
97 </when>
85 </conditional> 98 </conditional>
86 99
87 <conditional name="job_type"> 100 <conditional name="job_type">
88 <param name="job" type="select" label="MLST or Gene Presence/Absence?"> 101 <param name="job" type="select" label="MLST, MLST with ST, or Gene Presence/Absence?">
89 <option value="none">none</option> 102 <option value="nost">MLST</option>
90 <option value="mlst">MLST</option> 103 <option value="mlst">MLST with ST Definitions</option>
91 <option value="gene">Gene</option> 104 <option value="gene">Gene</option>
92 </param> 105 </param>
106 <when value="nost">
107 <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />
108 <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default &apos;_&apos;)" />
109 <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read" />
110 </when>
93 <when value="mlst"> 111 <when value="mlst">
94 <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" /> 112 <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />
95 <param type="data" name="mlst_definitions" label="ST definitions for MLST scheme" format="tabular" /> 113 <param type="data" name="mlst_definitions" label="ST definitions for MLST scheme" format="tabular" />
96 <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default &apos;_&apos;)" /> 114 <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default &apos;_&apos;)" />
97 <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read" /> 115 <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read" />