# HG changeset patch
# User estrain
# Date 1559041623 14400
# Node ID ba3ddf429854fbc13c50eb2045c76f091e94ac2a
# Parent  53b629d3da6866a1861a0ad9f9cdddaf2f618b2b
Uploaded

diff -r 53b629d3da68 -r ba3ddf429854 srst2v2.xml
--- a/srst2v2.xml	Mon May 20 13:55:36 2019 -0400
+++ b/srst2v2.xml	Tue May 28 07:07:03 2019 -0400
@@ -15,7 +15,8 @@
             ln -s $paired_conditional.fastq1 sample_1.fastq;
             ln -s $paired_conditional.fastq2 sample_2.fastq;
           #end if
-	#else if $paired_conditional.sPaired == "paired_coll" 
+          #set fname=$paired_conditional.fastq1.name
+        #else if $paired_conditional.sPaired == "paired_coll" 
 	  #if $paired_conditional.coll.forward.is_of_type("fastq.gz")
             zcat $paired_conditional.coll.forward > sample_1.fastq;
             zcat $paired_conditional.coll.reverse > sample_2.fastq;
@@ -26,7 +27,8 @@
             ln -s $paired_conditional.coll.forward sample_1.fastq;
             ln -s $paired_conditional.coll.reverse sample_2.fastq;
           #end if
-	#else if $paired_conditional.sPaired == "single"
+          #set fname=$paired_conditional.coll.forward.name
+        #else if $paired_conditional.sPaired == "single"
 	  #if $paired_conditional.fastq1.is_of_type("fastq.gz")
             zcat $paired_conditional.fastq1 > sample_1.fastq;
 	  #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
@@ -34,12 +36,13 @@
           #else
             ln -s $paired_conditional.fastq1 sample_1.fastq;
           #end if
+          #set fname=$paired_conditional.fastq1.name
         #end if
 
         srst2
 
         #if $paired_conditional.sPaired == "single"
-            --input_se sample_1.fastq
+            --input_se sample_1.fastq1
         #else
             --input_pe sample_1.fastq sample_2.fastq
         #end if
@@ -96,6 +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
@@ -173,16 +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>