--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityrnaseq.xml	Mon Jul 16 09:18:23 2012 -0400
@@ -0,0 +1,127 @@
+<tool id="trinityrnaseq" name="Trinity" version="0.0.1">
+
+    <!-- Written by Jeremy Goecks, now maintained here by bhaas -->
+    <description>De novo assembly of RNA-Seq data Using Trinity</description>
+    <requirements>
+        <requirement type="package">trinity</requirement>
+    </requirements>
+    <command>
+        Trinity.pl --JM $JM --CPU $CPU
+        
+        ## Inputs.
+        #if str($inputs.paired_or_single) == "paired":
+            --left $inputs.left_input --right $inputs.right_input
+            #if  $inputs.left_input.ext == 'fa':
+                --seqType fa
+            #else:
+                --seqType fq
+            #end if
+            #if str($inputs.library_type) != "None":
+                --SS_lib_type $inputs.library_type
+            #end if
+			--group_pairs_distance $inputs.group_pairs_distance
+        #else:
+            --single $inputs.input
+            #if  str($inputs.input.ext) == 'fa':
+                --seqType fa
+            #else:
+                --seqType fq
+            #end if
+            #if str($inputs.library_type) != "None":
+                --SS_lib_type $inputs.library_type
+            #end if
+        #end if
+
+        ## Additional parameters.
+        #if str($additional_params.use_additional) == "yes":
+			--min_kmer_cov $inputs.min_kmer_cov --max_reads_per_graph $inputs.max_reads_per_graph --bflyHeapSpaceMax $input.bflyHeapSpaceMax
+			#if $inputs.bfly_opts != 'None':
+				--bfly_opts " $inputs.bfly_opts "
+			#end if
+        #end if
+	
+                
+        ## direct to output
+        > $trinity_log 2>&amp;1
+ 
+    </command>
+    <inputs>
+      	<param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
+			<option value="1G">1G</option>
+			<option value="10G">10G</option>
+			<option value="50G">50G</option>
+			<option value="100G">100G</option>
+			<option value="200G">200G</option>
+			<option value="500G">500G</option>
+		</param>
+
+		<param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by Trinity" />
+
+
+        <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,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
+                <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
+                <param name="library_type" type="select" label="Strand-specific Library Type">
+                    <option value="None">None</option>
+                    <option value="FR">FR</option>
+                    <option value="RF">RF</option>
+                </param>
+                <param name="group_pairs_distance" type="integer" value="500" min="1" label="Group pairs distance" help="Maximum length expected between fragment pairs"/>
+		        <param name="path_reinforcement_distance" type="integer" value="75" min="1" label="Path reinforcement distance" help="Minimum read overlap required for path extension in the graph" />    
+
+            </when>
+            <when value="single">
+                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
+                <param name="library_type" type="select" label="Strand-specific Library Type">
+                    <option value="None">None</option>
+                    <option value="F">F</option>
+                    <option value="R">R</option>
+                </param>
+	            <param name="path_reinforcement_distance" type="integer" value="40" min="1" label="Path reinforcement distance" help="Minimum read overlap required for path extension in the graph" />    
+            </when>
+        </conditional>
+    	
+		<conditional name="additional_params">
+            <param name="use_additional" type="select" label="Use Additional Params?">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">            
+				<param name="min_kmer_cov" type="integer" value="1" min="1" label="inchworm_min_kmer_cov" help="Minimum kmer coverage required by Inchworm for initial contig construction" />
+				<param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" />
+				
+			
+				<param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" />
+				<param name="bflyHeapSpaceMax" type="select" label="bflyHeapSpaceMax" help="Java heap space maximum value for Butterfly">
+					<option value="1G">1G</option>
+					<option value="2G">2G</option>
+					<option value="4G" selected="true">4G</option>
+					<option value="10G">10G</option>
+					<option value="20G">20G</option>
+				</param>
+
+               <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
+            </when>
+        </conditional>
+    
+
+    </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>
+    </tests>
+    <help>
+        Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass.
+        
+        .. _Trinity: http://trinityrnaseq.sourceforge.net
+    </help>
+</tool>