# HG changeset patch
# User estrain
# Date 1558265815 14400
# Node ID 6787d952242ee7e8bdaf23fd713098d4e11897df
# Parent  43cc60256036c683f68d70f678eeb7ac426d174a
Uploaded

diff -r 43cc60256036 -r 6787d952242e srst2v2.xml
--- a/srst2v2.xml	Sat May 18 19:09:56 2019 -0400
+++ b/srst2v2.xml	Sun May 19 07:36:55 2019 -0400
@@ -1,11 +1,14 @@
-<tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.3">
+<tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0">
     <requirements>
-        <requirement type="package" version="0.2.3">srst2</requirement>
+        <requirement type="package" version="0.2.0">srst2</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if $paired_conditional.sPaired == "paired"
            ln -s $paired_conditional.fastq1 sample_1.fastq;
            ln -s $paired_conditional.fastq2 sample_2.fastq;
+        #else if $paired_conditional.sPaired == "paired_coll" 
+           ln -s $paired_conditional.coll.forward sample_1.fastq;
+           ln -s $paired_conditional.coll.reverse sample_2.fastq;
         #end if
 
         srst2
@@ -14,6 +17,8 @@
             --input_se $paired_conditional.fastq1
         #else if $paired_conditional.sPaired == "paired"
             --input_pe sample_1.fastq sample_2.fastq
+        #else if $paired_conditional.sPaired == "paired_coll"
+            --input_pe sample_1.fastq sample_2.fastq
         #end if
 
         --output srst2out 
@@ -27,6 +32,10 @@
         #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"
@@ -72,8 +81,9 @@
     <inputs>
       <conditional name="paired_conditional">
         <param name="sPaired" type="select" label="Single-End or Paired-End FASTQ?">
-          <option value="single">Single-end</option>
-          <option value="paired">Paired-end</option>
+          <option value="single">Single FASTQ</option>
+          <option value="paired">Forward and Reverse FASTQ</option>
+          <option value="paired_coll">Paired FASTQ Collection</option>
         </param>
         <when value="single">
           <param name="fastq1" type="data" format="fastq,fastqsanger" label="FASTQ file" help="FASTQ" />
@@ -82,14 +92,22 @@
           <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>
+        <when value="paired_coll">
+          <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger" collection_type="paired" />
+        </when>
       </conditional>
 
       <conditional name="job_type">
-        <param name="job" type="select" label="MLST or Gene Presence/Absence?">
-          <option value="none">none</option>
-          <option value="mlst">MLST</option>
+        <param name="job" type="select" label="MLST, MLST with ST, or Gene Presence/Absence?">
+          <option value="nost">MLST</option>
+          <option value="mlst">MLST with ST Definitions</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" />