# HG changeset patch
# User iuc
# Date 1449663592 18000
# Node ID 0067c78f49dc83c7052fe22dd9873348378a51df
# Parent  606b7748965d94d43e806a30fc61c994b909b95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64

diff -r 606b7748965d -r 0067c78f49dc tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Nov 20 06:50:00 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 09 07:19:52 2015 -0500
@@ -6,8 +6,8 @@
     <package name="bowtie" version="1.1.2">
         <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <set_environment version="1.0">
         <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">--max_memory 30G --bflyHeapSpaceMax 30G</environment_variable>
diff -r 606b7748965d -r 0067c78f49dc trinity.xml
--- a/trinity.xml	Fri Nov 20 06:50:00 2015 -0500
+++ b/trinity.xml	Wed Dec 09 07:19:52 2015 -0500
@@ -1,10 +1,10 @@
-<tool id="trinity" name="Trinity" version="2.0.6">
+<tool id="trinity" name="Trinity" version="2.0.6.1">
     <description>de novo assembly of RNA-Seq data</description>
     <requirements>
         <requirement type="package" version="2.0.6">trinity</requirement>
         <requirement type="package" version="1.1.2">bowtie</requirement>
-        <requirement type="package" version="0.1.19">samtools</requirement>
-        <requirement type="set_environment">TRINITY_MAX_MEMORY</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
     </requirements>
     <command><![CDATA[
        Trinity
@@ -48,7 +48,7 @@
         #if $additional_params.long_reads:
             --long_reads $additional_params.long_reads
         #end if
-        #if $additional_params.guided.is_guided == "yes" and $additional_params.guided.genome_guided_bam:
+        #if $additional_params.guided.is_guided == "yes":
             --genome_guided_bam $additional_params.guided.genome_guided_bam
 
             #if $additional_params.guided.genome_guided_min_coverage:
@@ -112,14 +112,14 @@
             <param name="min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
             
             <conditional name="guided">
-                <param name="is_guided" type="select" label="Use the genome guided mode?" help="">
+                <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information">
                     <option value="no">No</option>
                     <option value="yes">Yes</option>
                  </param>
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <param format="bam" name="genome_guided_bam" type="data" optional="true" label="Genome guided BAM file" help="If you already mapped the reads to the genome, trinity can use this information"/>
+                    <param format="bam" name="genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
                     <param name="genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
                     <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
                 </when>