# HG changeset patch
# User estrain
# Date 1559001271 14400
# Node ID c86195daec93b86780c39ef908ed404b1d6a4b41
# Parent  3a0554ef7cc29bb809b502c29ef6d9ebd2b62909
Uploaded

diff -r 3a0554ef7cc2 -r c86195daec93 srst2v2.xml
--- a/srst2v2.xml	Sun May 19 10:00:38 2019 -0400
+++ b/srst2v2.xml	Mon May 27 19:54:31 2019 -0400
@@ -96,8 +96,10 @@
           --other "'-p \${GALAXY_SLOTS:-1}'"
       #end if
 
+      ; cat *results.txt | sed /sample/${name}/ > results.txt
+
       #if $job_type.job == "mlst" 
-        ; python $__tool_directory__/scoreProfiles.py --mlst_definitions $job_type.mlst_definitions --profile_cov $job_type.profile_cov --profile_max_mismatch $job_type.profile_max_mismatch --output srst2.pscores
+        ; python $__tool_directory__/scoreProfiles.py --mlst_definitions $job_type.mlst_definitions --profile_cov $job_type.profile_cov --profile_max_mismatch $job_type.profile_max_mismatch --output srst2.pscores ; cat srst2.pscores | sed s/sample/${name}/ > srst2.pscores  
       #end if
 
     ]]></command>
@@ -109,14 +111,14 @@
           <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" />
+          <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file" help="FASTQ" />
         </when>
         <when value="paired">
-          <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" />
+          <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Forward FASTQ file" help="FASTQ" />
+          <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" 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" />
+          <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
         </when>
       </conditional>