--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinity.xml	Fri Nov 20 06:50:00 2015 -0500
@@ -0,0 +1,166 @@
+<tool id="trinity" name="Trinity" version="2.0.6">
+    <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>
+    </requirements>
+    <command><![CDATA[
+       Trinity
+
+        ## Inputs.
+        #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
+            
+            $inputs.jaccard_clip
+
+        #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
+            
+        $norm
+
+        ## Additional parameters.
+        #if $additional_params.min_contig_length:
+            --min_contig_length $additional_params.min_contig_length
+        #end if
+        #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:
+            --genome_guided_bam $additional_params.guided.genome_guided_bam
+
+            #if $additional_params.guided.genome_guided_min_coverage:
+                --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
+            #end if
+
+            #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} --bfly_opts "-V 10 --stderr"
+        
+         > $trinity_log 2>&1
+
+    ]]></command>
+    <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>
+            </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=""/>
+                <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" type="select" label="Strand-specific Library Type">
+                            <option value="FR">Forward-Reverse</option>
+                            <option value="RF">Reverse-Forward</option>
+                        </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=""/>
+                <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" type="select" label="Strand-specific Library Type">
+                            <option value="F">F</option>
+                            <option value="R">R</option>
+                        </param>
+                    </when>
+                </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="">
+                    <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 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>
+            </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>
+    <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"/>
+    </outputs>
+    <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="is_strand_specific" value="true"/>
+            <param name="norm" value="false"/>
+            <param name="library_type" value="RF"/>
+            <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
+        </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="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: http://trinityrnaseq.github.io
+    </help>
+    
+     <citations>
+        <citation type="doi">doi:10.1038/nbt.1883</citation>
+    </citations>
+</tool>
+