# HG changeset patch
# User estrain
# Date 1559040480 14400
# Node ID 5cfca4d5291a9aa787b8d7031733f1b2b2bd6eb5
# Parent  a2c25a81368b5e634bea23172c6c4407336c3691
Uploaded

diff -r a2c25a81368b -r 5cfca4d5291a srst2v2.xml
--- a/srst2v2.xml	Tue May 28 06:31:14 2019 -0400
+++ b/srst2v2.xml	Tue May 28 06:48:00 2019 -0400
@@ -99,6 +99,8 @@
           --other "'-p \${GALAXY_SLOTS:-1}'"
       #end if
 
+      ; cat *results.txt | sed s/sample/${fname}/ > cat_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
       #end if
@@ -176,16 +178,13 @@
     </inputs>
 
     <outputs>
-      <data format="tabular" label="SRST2 Results" name="results" from_work_dir="*.txt"/>
+      <data format="tabular" label="SRST2 Results" name="results" from_work_dir="*cat_results.txt"/>
       <data format="tabular" label="SRST2 Allele Scores" name="scores" from_work_dir="*.scores">
         <filter>job_type['job'] == "mlst"</filter>
       </data>  
       <data format="tabular" label="SRST2 Profile Scores" name="pscores" from_work_dir="*.pscores">
         <filter> job_type['job'] == "mlst"</filter>
       </data>  
-      <data format="tabular" label="SRST2 Predicted Alleles" name="alleles" from_work_dir="*results.txt">
-        <filter> job_type['job'] == "mlst"</filter>
-      </data>  
       <data format="tabular" label="SRST2 Gene Scores" name="gscores" from_work_dir="*.scores">
         <filter>job_type['job'] == "gene"</filter>
       </data>