# HG changeset patch
# User estrain
# Date 1558221428 14400
# Node ID 2b6c54603b6e9ce6ce502c021903b67a3404011e
# Parent  a98ed567ea48b408203e0d00097da75c4c455e16
Uploaded

diff -r a98ed567ea48 -r 2b6c54603b6e srst2v2.xml
--- a/srst2v2.xml	Sat Dec 02 21:23:44 2017 -0500
+++ b/srst2v2.xml	Sat May 18 19:17:08 2019 -0400
@@ -1,6 +1,6 @@
-<tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0">
+<tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.3">
     <requirements>
-        <requirement type="package" version="0.2.0">srst2</requirement>
+        <requirement type="package" version="0.2.3">srst2</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if $paired_conditional.sPaired == "paired"
@@ -27,6 +27,10 @@
         #else if $job_type.job == "gene"
           --gene_db $job_type.genedb
           --gene_max_mismatch $job_type.gene_max_mismatch
+        #else if $job_type.job == "nost"
+          --mlst_db $job_type.mlst_db 
+          --mlst_delimiter $job_type.mlstdelim
+          --mlst_max_mismatch $job_type.mlst_max_mismatch
         #end if
 
         #if $options.select == "advanced"
@@ -76,19 +80,25 @@
           <option value="paired">Paired-end</option>
         </param>
         <when value="single">
-          <param name="fastq1" type="data" format="fastq" label="FASTQ file" help="FASTQ" />
+          <param name="fastq1" type="data" format="fastq,fastqsanger" label="FASTQ file" help="FASTQ" />
         </when>
         <when value="paired">
-          <param name="fastq1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ" />
-          <param name="fastq2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ" />
+          <param name="fastq1" type="data" format="fastq,fastqsanger" label="Forward FASTQ file" help="FASTQ" />
+          <param name="fastq2" type="data" format="fastq,fastqsanger" label="Reverse FASTQ file" help="FASTQ" />
         </when>
       </conditional>
 
       <conditional name="job_type">
         <param name="job" type="select" label="MLST or Gene Presence/Absence?">
-          <option value="mlst">MLST</option>
+          <option value="nost">MLST</option>
+          <option value="mlst">MLST with ST</option>
           <option value="gene">Gene</option>
         </param>
+        <when value="nost">
+          <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />
+          <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default &apos;_&apos;)" />
+          <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read" />
+        </when> 
         <when value="mlst">
           <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />
           <param type="data" name="mlst_definitions" label="ST definitions for MLST scheme" format="tabular" />