# HG changeset patch
# User ycogne
# Date 1480670004 18000
# Node ID 38461a69ece5697d37ebc2ba0d11f2b83175dfed

Uploaded

diff -r 000000000000 -r 38461a69ece5 bridger.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bridger.xml	Fri Dec 02 04:13:24 2016 -0500
@@ -0,0 +1,104 @@
+<tool id="bridger" name="bridger" version="v1">
+	<description>de novo assembly of RNA-Seq data</description>
+	<requirements>
+	<container type="docker">ycogne/bridger</container>
+  </requirements>
+	<command>
+	   /usr/bin/Bridger_r2014-12-01/Bridger.pl 
+	  
+		#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
+
+		--CPU $additional_params.CPU_usage
+		-k $additional_params.kmer_used 
+	   
+	   -o /home/results/Bridger	2>1 ;
+	   mv /home/results/Bridger/Bridger.fasta $assembled_transcripts
+
+	   
+
+	</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,fastq" argument="--left" name="left_input"  type="data" label="Left/Forward strand reads" help=""/>
+				<param format="fasta,fastqsanger,fastq" argument="--right" 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" 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>
+			 </when>
+			<when value="single">
+				<param format="fasta,fastqsanger,fastq" name="input" argument="--single"  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" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
+							<option value="F">F</option>
+							<option value="R">R</option>
+						</param>
+					</when>
+				</conditional>
+			</when>
+		</conditional>
+	 
+	  <section name="additional_params" title="Additional Options" expanded="False">
+					<param name="CPU_usage" argument="--CPU_usage" type="integer" optional="true" value="3" min="1" label="Number of CPU" help="Number of CPU use by the software"/>
+					<param name="kmer_used" argument="-k" type="integer" optional="true" value="25" min="10" label="Kmer length" help="Kmer length"/>
+
+		</section>
+	 
+		</inputs>
+	<outputs>
+	
+		  <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" />
+	 
+	</outputs>
+	<help>
+	  https://github.com/fmaguire/Bridger_Assembler
+	</help>
+
+	
+</tool>