# HG changeset patch
# User iuc
# Date 1604503967 0
# Node ID 103bd59b3e33fb2c839cebe83e5ad6ff8f541cfa
# Parent  58234d95978d3fe94d356f053caf3dfd57124487
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 6a29aaead9d6b0f69ef70113df58047877fc6ce5"

diff -r 58234d95978d -r 103bd59b3e33 bacteria_tradis.xml
--- a/bacteria_tradis.xml	Fri Feb 07 05:20:39 2020 -0500
+++ b/bacteria_tradis.xml	Wed Nov 04 15:32:47 2020 +0000
@@ -4,7 +4,7 @@
           <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command>
+    <command detect_errors="aggressive">
         <![CDATA[
             ls '${input_fastq}' > file.txt &&
             bacteria_tradis -v -f file.txt -r  '${input_ref}'
diff -r 58234d95978d -r 103bd59b3e33 tradis_essentiality.xml
--- a/tradis_essentiality.xml	Fri Feb 07 05:20:39 2020 -0500
+++ b/tradis_essentiality.xml	Wed Nov 04 15:32:47 2020 +0000
@@ -4,25 +4,21 @@
           <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command>
+    <command detect_errors="aggressive">
         <![CDATA[
             ln -s '$input_insert_file' input.csv &&
-            tradis_essentiality.R input.csv 
+            tradis_essentiality.R input.csv
         ]]>
     </command>
-    
     <inputs>
         <param name="input_insert_file" type="data" format="csv" label="Gene insertion counts" help="Ourput file of `Bio-TraDis counts to gene insertion data` tool"/>
     </inputs>
-    
     <outputs>
-
-        <data name="ess_genes" format="csv" label="${tool.name} on ${on_string} : Essential genes" from_work_dir="input.csv.essen.csv"/>
-        <data name="ambig_genes" format="csv" label="${tool.name} on ${on_string} : Unclassified genes" from_work_dir="input.csv.ambig.csv"/>
-        <data name="all_genes" format="csv" label="${tool.name} on ${on_string} : All genes" from_work_dir="input.csv.all.csv"/>
-        <data name="qc_results" format="pdf" label="${tool.name} on ${on_string} : QC report" from_work_dir="input.csv.QC_and_changepoint_plots.pdf"/>
+        <data name="ess_genes" format="csv" label="${tool.name} on ${on_string}: Essential genes" from_work_dir="input.csv.essen.csv"/>
+        <data name="ambig_genes" format="csv" label="${tool.name} on ${on_string}: Unclassified genes" from_work_dir="input.csv.ambig.csv"/>
+        <data name="all_genes" format="csv" label="${tool.name} on ${on_string}: All genes" from_work_dir="input.csv.all.csv"/>
+        <data name="qc_results" format="pdf" label="${tool.name} on ${on_string}: QC report" from_work_dir="input.csv.QC_and_changepoint_plots.pdf"/>
     </outputs>
-    
     <tests>
         <test>
             <param name="input_insert_file" ftype="csv" value="test.csv"/>
diff -r 58234d95978d -r 103bd59b3e33 tradis_gene_insert_sites.xml
--- a/tradis_gene_insert_sites.xml	Fri Feb 07 05:20:39 2020 -0500
+++ b/tradis_gene_insert_sites.xml	Wed Nov 04 15:32:47 2020 +0000
@@ -4,7 +4,7 @@
           <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command>
+    <command detect_errors="aggressive">
         <![CDATA[
             tradis_gene_insert_sites -trim3 '$trim3' -trim5 '$trim5' '$input_annot' '$input_counts'  
         ]]>