# HG changeset patch
# User iuc
# Date 1513342405 18000
# Node ID 87ab70ffdf1f38fa53a9a35973ed315e22a2e68f
# Parent  b9b604bcd85b287bfc08bf3736c573ec78e2dba1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58

diff -r b9b604bcd85b -r 87ab70ffdf1f README.rst
--- a/README.rst	Mon Aug 28 16:49:49 2017 -0400
+++ b/README.rst	Fri Dec 15 07:53:25 2017 -0500
@@ -9,22 +9,22 @@
 By default, this tool is configured to limit the memory consumption to 1G.
 You might need to lower this limit if the machine(s) executing the jobs have less memory available.
 If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
-In both cases, you can set the TRINITY_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file:
+In both cases, you can set the TRINITY_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file::
 
-<?xml version="1.0"?>
-<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
-    </plugins>
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-    <destinations>
-        <destination id="local" runner="local">
-            <env id="TRINITY_MAX_MEMORY">1G</env>
-        </destination>
-    </destinations>
-</job_conf>
+    <?xml version="1.0"?>
+    <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
+    <job_conf>
+        <plugins>
+            <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+        </plugins>
+        <handlers>
+            <handler id="main"/>
+        </handlers>
+        <destinations>
+            <destination id="local" runner="local">
+                <env id="TRINITY_MAX_MEMORY">1G</env>
+            </destination>
+        </destinations>
+    </job_conf>
 
 
diff -r b9b604bcd85b -r 87ab70ffdf1f macros.xml
--- a/macros.xml	Mon Aug 28 16:49:49 2017 -0400
+++ b/macros.xml	Fri Dec 15 07:53:25 2017 -0500
@@ -9,6 +9,28 @@
 
     <token name="@WRAPPER_VERSION@">2.4.0</token>
 
+    <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
+        #if $inputs.strand.is_strand_specific:
+            --SS_lib_type $inputs.strand.library_type
+        #end if
+
+        $inputs.jaccard_clip
+    </token>
+
+    <xml name="input_paired_strand_jaccard">
+        <conditional name="strand">
+            <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+            <when value="false" />
+            <when value="true">
+                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
+                    <option value="FR">Forward-Reverse</option>
+                    <option value="RF">Reverse-Forward</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="jaccard_clip" argument="--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"/>
+    </xml>
+
     <xml name="citation">
         <citations>
             <citation type="doi">10.1038/nbt.1883</citation>
diff -r b9b604bcd85b -r 87ab70ffdf1f trinity.xml
--- a/trinity.xml	Mon Aug 28 16:49:49 2017 -0400
+++ b/trinity.xml	Fri Dec 15 07:53:25 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0">
+<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.1">
     <description>de novo assembly of RNA-Seq data</description>
     <macros>
         <import>macros.xml</import>
@@ -20,11 +20,20 @@
                 --seqType fq
             #end if
 
-            #if $inputs.strand.is_strand_specific:
-                --SS_lib_type $inputs.strand.library_type
+            @COMMAND_PAIRED_STRAND_JACCARD@
+
+        #elif $inputs.paired_or_single == "paired_collection"
+            --left ${ ','.join(['"%s"' % x.forward for x in $inputs.pair_input]) }
+
+            --right ${ ','.join(['"%s"' % x.reverse for x in $inputs.pair_input]) }
+
+            #if $inputs.pair_input[0].forward.is_of_type('fasta'):
+                --seqType fa
+            #else:
+                --seqType fq
             #end if
 
-            $inputs.jaccard_clip
+            @COMMAND_PAIRED_STRAND_JACCARD@
 
         #else:
             --single ${ ','.join(['"%s"' % x for x in $inputs.input]) }
@@ -74,27 +83,12 @@
     <inputs>
         <conditional name="inputs">
             <param name="paired_or_single" type="select" label="Paired or Single-end data?">
-                <option value="paired">Paired</option>
-                <option value="single">Single</option>
+                <option value="single">Single-end</option>
+                <option value="paired" selected="true">Paired-end</option>
+                <option value="paired_collection">Paired-end collection</option>
             </param>
-            <when value="paired">
-                <param format="fasta,fastqsanger" argument="--left" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/>
-                <param format="fasta,fastqsanger" argument="--right" name="right_input" multiple="true" type="data" label="Right/Reverse strand reads" help=""/>
-                <conditional name="strand">
-                    <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
-                    <when value="false">
-                    </when>
-                    <when value="true">
-                        <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
-                            <option value="FR">Forward-Reverse</option>
-                            <option value="RF">Reverse-Forward</option>
-                        </param>
-                    </when>
-                </conditional>
-                <param name="jaccard_clip" argument="--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,fastqsanger" name="input" argument="--single" multiple="true" type="data" label="Single-end reads" help=""/>
+                <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/>
                 <conditional name="strand">
                     <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                     <when value="false">
@@ -107,6 +101,15 @@
                     </when>
                 </conditional>
             </when>
+            <when value="paired">
+                <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" />
+                <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" />
+                <expand macro="input_paired_strand_jaccard" />
+            </when>
+            <when value="paired_collection">
+                <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/>
+                <expand macro="input_paired_strand_jaccard" />
+            </when>
         </conditional>
 
         <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
@@ -122,20 +125,19 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
+                    <param name="genome_guided_bam" argument="--genome_guided_bam" type="data" format="bam" label="Coordinate-sorted BAM file" />
                     <param name="genome_guided_min_coverage" argument="--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" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
                 </when>
             </conditional>
 
-            <param format="fasta" name="long_reads" argument="--long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
+            <param name="long_reads" argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
 
             <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
         </section>
     </inputs>
     <outputs>
-        <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /-->
-        <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
+        <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
     </outputs>
     <tests>
         <test>
@@ -156,11 +158,34 @@
             <param name="library_type" value="RF"/>
             <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
         </test>
+        <test>
+            <param name="paired_or_single" value="paired_collection"/>
+            <param name="pair_input">
+                <collection type="list:paired">
+                    <element name="pair1">
+                        <collection type="paired">
+                            <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
+                            <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
+                        </collection>
+                    </element>
+                    <element name="pair2">
+                        <collection type="paired">
+                            <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
+                            <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
+                        </collection>
+                    </element>
+                </collection>
+            </param>
+            <param name="is_strand_specific" value="true"/>
+            <param name="norm" value="true"/>
+            <param name="library_type" value="RF"/>
+            <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
+        </test>
     </tests>
     <help>
-        Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
 
-        .. _Trinity: http://trinityrnaseq.github.io
+.. _Trinity: http://trinityrnaseq.github.io
     </help>
 
     <expand macro="citation" />