diff trinity.xml @ 2:de0af39266ef draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45

--- a/trinity.xml	Wed Dec 09 07:19:52 2015 -0500
+++ b/trinity.xml	Mon Apr 25 10:02:37 2016 -0400
@@ -1,7 +1,7 @@
-<tool id="trinity" name="Trinity" version="2.0.6.1">
+<tool id="trinity" name="Trinity" version="2.1.1">
     <description>de novo assembly of RNA-Seq data</description>
     <requirements>
-        <requirement type="package" version="2.0.6">trinity</requirement>
+        <requirement type="package" version="2.1.1">trinity</requirement>
         <requirement type="package" version="1.1.2">bowtie</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
         <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
@@ -62,9 +62,9 @@
         #end if
 
         ## CPU and butterfly options.
-        --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS} --bfly_opts "-V 10 --stderr"
+        --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
         
-         > $trinity_log 2>&1
+        ## > $trinity_log 2>&1
 
     ]]></command>
     <inputs>
@@ -87,11 +87,10 @@
                         </param>
                     </when>
                 </conditional>
-                <param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/>
                 <param name="jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/>
             </when>
             <when value="single">
-                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
+                <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/>
                 <conditional name="strand">
                     <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                     <when value="false">
@@ -130,7 +129,7 @@
         </section>
     </inputs>
     <outputs>
-        <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
+        <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /-->
         <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
     </outputs>
     <tests>