diff trinityrnaseq.xml @ 1:a34ce2b18877 draft

Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie

--- a/trinityrnaseq.xml	Wed Mar 20 09:17:14 2013 -0400
+++ b/trinityrnaseq.xml	Fri Aug 30 10:56:26 2013 -0500
@@ -1,8 +1,10 @@
-<tool id="trinityrnaseq" name="Trinity" version="0.0.1">
+<tool id="trinityrnaseq" name="Trinity" version="0.0.2">
     <!-- Written by Jeremy Goecks, now maintained here by bhaas -->
     <description>De novo assembly of RNA-Seq data Using Trinity</description>
     <requirements>
-        <requirement type="package" version="2013-02-25">trinityrnaseq</requirement>
+        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="1.0.0">bowtie</requirement>
     </requirements>
     <command>
         Trinity.pl --JM $JM --CPU $CPU
@@ -41,7 +43,7 @@
 	
                 
         ## direct to output
-        > $trinity_log 2>&amp;1
+        | tee $trinity_log | grep 'Error'
  
     </command>
     <inputs>
@@ -109,6 +111,14 @@
     </inputs>
     <stdio>
         <exit_code range="1:"  level="fatal"   description="Faiiled" />
+        <regex match="command not found" 
+               source="both" 
+               level="fatal" 
+               description="Trinity.pl not found" />
+        <regex match="Error" 
+               source="both" 
+               level="fatal" 
+               description="A trinity process failed" />
     </stdio>
     <outputs>
         <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />