# HG changeset patch
# User iuc
# Date 1462287265 14400
# Node ID c7555bc218124085db30167e3c7de392cae20476
# Parent  de0af39266efde1fcf283f19b236a0dcfb41cba2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b

diff -r de0af39266ef -r c7555bc21812 abundance_estimates_to_matrix.xml
--- a/abundance_estimates_to_matrix.xml	Mon Apr 25 10:02:37 2016 -0400
+++ b/abundance_estimates_to_matrix.xml	Tue May 03 10:54:25 2016 -0400
@@ -26,13 +26,13 @@
         #end for
     ]]></command>
     <inputs>
-        <repeat name="samples" title="RSEM abundance estimates for samples">
+        <repeat name="samples" title="Abundance estimates for samples">
             <param name="file" label="Add file" type="data" format="tabular"/>
             <param name="sample_name" label="Sample name" type="text">
                 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
             </param>
         </repeat>
-        
+
         <param type="select" name="est_method" label="Abundance estimation method">
             <option value="RSEM">RSEM</option>
             <option value="eXpress">eXpress</option>
@@ -198,7 +198,7 @@
 .. _Trinity: http://trinityrnaseq.github.io
 ]]>
     </help>
-    
+
      <citations>
         <citation type="doi">doi:10.1038/nbt.1883</citation>
     </citations>
diff -r de0af39266ef -r c7555bc21812 align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Mon Apr 25 10:02:37 2016 -0400
+++ b/align_and_estimate_abundance.xml	Tue May 03 10:54:25 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1">
+<tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1.1">
     <description>on a de novo assembly of RNA-Seq data</description>
     <requirements>
         <requirement type="package" version="2.1.1">trinity</requirement>
@@ -17,7 +17,7 @@
         &&
 
         align_and_estimate_abundance.pl
-       
+
         --transcripts input.fa
 
         --est_method $method.est_method
@@ -27,42 +27,42 @@
 
         #if $inputs.paired_or_single == "paired":
             --left $inputs.left_input --right $inputs.right_input
-            
+
             #if $inputs.left_input.is_of_type('fasta'):
                 --seqType fa
             #else:
                 --seqType fq
             #end if
-            
+
             #if $inputs.strand.is_strand_specific:
                 --SS_lib_type $inputs.strand.library_type
             #end if
 
         #else:
             --single $inputs.input
-            
+
             #if $inputs.input.is_of_type('fasta'):
                 --seqType fa
             #else:
                 --seqType fq
             #end if
-            
+
             #if $inputs.strand.is_strand_specific:
                 --SS_lib_type $inputs.strand.library_type
             #end if
         #end if
-        
+
         --max_ins_size $inputs.paired_fragment_length
 
         ## Additional parameters.
-        #if $additional_params.gene_map.has_gene_map == "yes":
+        #if $additional_params.gene_map.has_gene_map == "no":
             --gene_trans_map $additional_params.gene_map.gene_trans_map
         #else
             --trinity_mode
         #end if
-        
+
         --prep_reference
-        
+
         --output_dir .
 
         ## CPU
@@ -106,7 +106,7 @@
                 </conditional>
             </when>
         </conditional>
-        
+
         <conditional name="method">
             <param type="select" name="est_method" label="Abundance estimation method">
                 <option value="RSEM">RSEM</option>
@@ -129,16 +129,16 @@
         <section name="additional_params" title="Additional Options" expanded="False">
             <conditional name="gene_map">
                 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed">
+                    <option value="yes">Yes</option>
                     <option value="no">No</option>
-                    <option value="yes">Yes</option>
                 </param>
-                <when value="no">
+                <when value="yes">
                 </when>
-                <when value="yes">
+                <when value="no">
                     <param format="tabular" name="gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
                 </when>
             </conditional>
-            
+
         </section>
     </inputs>
     <outputs>
@@ -148,7 +148,7 @@
         <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="RSEM.genes.results">
             <filter>method['est_method'] == "RSEM"</filter>
         </data>
-        
+
         <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="results.xprs">
             <filter>method['est_method'] == "eXpress"</filter>
         </data>
@@ -165,7 +165,7 @@
             <param name="library_type" value="RF"/>
             <param name="est_method" value="RSEM"/>
             <param name="aln_method" value="bowtie"/>
-            <param name="has_gene_map" value="no"/>
+            <param name="has_gene_map" value="yes"/>
             <output name="isoforms_counts_rsem">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
@@ -187,7 +187,7 @@
             <param name="library_type" value="RF"/>
             <param name="est_method" value="RSEM"/>
             <param name="aln_method" value="bowtie2"/>
-            <param name="has_gene_map" value="no"/>
+            <param name="has_gene_map" value="yes"/>
             <output name="isoforms_counts_rsem">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
@@ -209,7 +209,7 @@
             <param name="library_type" value="RF"/>
             <param name="est_method" value="eXpress"/>
             <param name="aln_method" value="bowtie"/>
-            <param name="has_gene_map" value="no"/>
+            <param name="has_gene_map" value="yes"/>
             <output name="isoforms_counts_express">
                 <assert_contents>
                     <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />
@@ -252,7 +252,7 @@
 .. _Trinity: http://trinityrnaseq.github.io
 ]]>
     </help>
-    
+
      <citations>
         <citation type="doi">doi:10.1038/nbt.1883</citation>
     </citations>
diff -r de0af39266ef -r c7555bc21812 run_DE_analysis.xml
--- a/run_DE_analysis.xml	Mon Apr 25 10:02:37 2016 -0400
+++ b/run_DE_analysis.xml	Tue May 03 10:54:25 2016 -0400
@@ -7,7 +7,7 @@
         <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
         <requirement type="package" version="3.12.0">edger</requirement>
         <requirement type="package" version="3.12.0">bioconductor-edger</requirement>
-        <requirement type="package" version="3.25.3">limma</requirement>
+        <requirement type="package" version="3.27.4">limma</requirement>
         <requirement type="package" version="3.27.4">bioconductor-limma</requirement>
     </requirements>
     <stdio>
diff -r de0af39266ef -r c7555bc21812 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Apr 25 10:02:37 2016 -0400
+++ b/tool_dependencies.xml	Tue May 03 10:54:25 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="trinity" version="2.1.1">
-        <repository changeset_revision="b66b28a11557" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="f75117647d9c" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <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" />
@@ -25,7 +25,7 @@
         <repository changeset_revision="7c305aa20292" name="package_r_limma_3_27_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="deseq2" version="1.10.0">
-       <repository changeset_revision="362a2224b1d2" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="56a98b4043fd" name="package_deseq2_1_10_0" 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 de0af39266ef -r c7555bc21812 trinity.xml
--- a/trinity.xml	Mon Apr 25 10:02:37 2016 -0400
+++ b/trinity.xml	Tue May 03 10:54:25 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="trinity" name="Trinity" version="2.1.1">
+<tool id="trinity" name="Trinity" version="2.1.1.1">
     <description>de novo assembly of RNA-Seq data</description>
     <requirements>
         <requirement type="package" version="2.1.1">trinity</requirement>
@@ -11,34 +11,37 @@
 
         ## Inputs.
         #if $inputs.paired_or_single == "paired":
-            --left $inputs.left_input --right $inputs.right_input
-            
-            #if $inputs.left_input.is_of_type('fasta'):
+
+            --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) }
+
+            --right ${ ','.join(['"%s"' % x for x in $inputs.right_input]) }
+
+            #if $inputs.left_input[0].is_of_type('fasta'):
                 --seqType fa
             #else:
                 --seqType fq
             #end if
-            
+
             #if $inputs.strand.is_strand_specific:
                 --SS_lib_type $inputs.strand.library_type
             #end if
-            
+
             $inputs.jaccard_clip
 
         #else:
-            --single $inputs.input
-            
-            #if $inputs.input.is_of_type('fasta'):
+            --single ${ ','.join(['"%s"' % x for x in $inputs.input]) }
+
+            #if $inputs.input[0].is_of_type('fasta'):
                 --seqType fa
             #else:
                 --seqType fq
             #end if
-            
+
             #if $inputs.strand.is_strand_specific:
                 --SS_lib_type $inputs.strand.library_type
             #end if
         #end if
-            
+
         $norm
 
         ## Additional parameters.
@@ -58,12 +61,12 @@
             #if $additional_params.guided.genome_guided_min_reads_per_partition:
                 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
             #end if
-            
+
         #end if
 
         ## CPU and butterfly options.
         --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
-        
+
         ## > $trinity_log 2>&1
 
     ]]></command>
@@ -74,8 +77,8 @@
                 <option value="single">Single</option>
             </param>
             <when value="paired">
-                <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
-                <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
+                <param format="fasta,fastqsanger" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/>
+                <param format="fasta,fastqsanger" 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">
@@ -90,7 +93,7 @@
                 <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,fastqsanger" name="input" type="data" label="Single-end reads" help=""/>
+                <param format="fasta,fastqsanger" name="input" multiple="true" 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">
@@ -104,12 +107,12 @@
                 </conditional>
             </when>
         </conditional>
-        
+
         <param name="norm" type="boolean" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
 
         <section name="additional_params" title="Additional Options" expanded="False">
             <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="If you already mapped the reads to the genome, Trinity can use this information">
                     <option value="no">No</option>
@@ -123,8 +126,8 @@
                     <param name="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" 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"/>
         </section>
     </inputs>
@@ -135,8 +138,8 @@
     <tests>
         <test>
             <param name="paired_or_single" value="paired"/>
-            <param name="left_input" value="reads.left.fq"/>
-            <param name="right_input" value="reads.right.fq"/>
+            <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
+            <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
             <param name="is_strand_specific" value="true"/>
             <param name="norm" value="false"/>
             <param name="library_type" value="RF"/>
@@ -144,8 +147,8 @@
         </test>
         <test>
             <param name="paired_or_single" value="paired"/>
-            <param name="left_input" value="reads.left.fq"/>
-            <param name="right_input" value="reads.right.fq"/>
+            <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
+            <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
             <param name="is_strand_specific" value="true"/>
             <param name="norm" value="true"/>
             <param name="library_type" value="RF"/>
@@ -157,7 +160,7 @@
 
         .. _Trinity: http://trinityrnaseq.github.io
     </help>
-    
+
      <citations>
         <citation type="doi">doi:10.1038/nbt.1883</citation>
     </citations>