diff trinity.xml @ 15:e65e640e6196 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933

--- a/trinity.xml	Thu Mar 23 10:15:32 2017 -0400
+++ b/trinity.xml	Fri Mar 31 11:35:34 2017 -0400
@@ -3,13 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.1.2">bowtie</requirement>
-        <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
-    </expand>
-    <expand macro="stdio"/>
-    <command><![CDATA[
-       Trinity
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+       Trinity --no_version_check
 
         ## Inputs.
         #if $inputs.paired_or_single == "paired":
@@ -71,10 +67,9 @@
         #end if
 
         ## CPU and butterfly options.
-        --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
+        --CPU \${GALAXY_SLOTS:-4} --max_memory \${TRINITY_MAX_MEMORY:-1G} --bflyHeapSpaceMax \${TRINITY_MAX_MEMORY:-1G} --bfly_opts '-V 10 --stderr'
 
         ## > $trinity_log 2>&1
-
     ]]></command>
     <inputs>
         <conditional name="inputs">