From dd7f9dc3a70ff674a52ca6fdc3c5555c70fd3453 Mon Sep 17 00:00:00 2001
From: Remi Marenco <remimarenco@gmail.com>
Date: Tue, 17 Jul 2012 17:12:51 -0400
Subject: [PATCH] eXpress tool wrapped in Galaxy. Added in "NGS: RNA Analysis".

---
 tool_conf.xml.sample              |  1 +
 tools/ngs_rna/express_wrapper.xml | 53 +++++++++++++++++++++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 tools/ngs_rna/express_wrapper.xml

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 27c13063cec..b94ffa3001e 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -361,6 +361,7 @@
     <tool file="ngs_rna/tophat_color_wrapper.xml" />
     <tool file="ngs_rna/cufflinks_wrapper.xml" />
     <tool file="ngs_rna/cuffcompare_wrapper.xml" />
+    <tool file="ngs_rna/express_wrapper.xml" />
  	<tool file="ngs_rna/cuffmerge_wrapper.xml" />
     <tool file="ngs_rna/cuffdiff_wrapper.xml" />
     <!-- Trinity is very memory-intensive and should only be enabled/run
diff --git a/tools/ngs_rna/express_wrapper.xml b/tools/ngs_rna/express_wrapper.xml
new file mode 100644
index 00000000000..a9389df8f55
--- /dev/null
+++ b/tools/ngs_rna/express_wrapper.xml
@@ -0,0 +1,53 @@
+<tool id="express" name="eXpress" version="1.1.1">
+	<description>Quantify the abundances of a set of target sequences from sampled subsequences</description>
+	<requirements>
+		<requirement type="binary">eXpress</requirement>
+	</requirements>
+	<command>express --no-update-check $multiFasta $bamFile</command>
+	<inputs>
+		<param format="fasta" name="multiFasta" type="data" label="A set of target references (annotation) in multi-FASTA format" help="The multi-FASTA file can also be a fasta file" />
+		<param format="bam" name="bamFile" type="data" label="Alignments in the BAM format" help="The set of aligned reads" />
+	</inputs>
+	<outputs>  
+       <data format="txt" name="params" from_work_dir="params.xprs"/>
+       <data format="txt" name="results" from_work_dir="results.xprs"/>
+   </outputs>
+
+   <tests>
+        <!-- Test for the most simple case : Running eXpress with a .bam file and a .fasta file -->
+        <test>
+            <!-- TopHat commands:
+            eXpress hits.bam Trinity.fasta
+            -->
+            <param name="bamFile" ftype="bam" value="eXpress_hits.bam"/>
+            <param name="multiFasta" ftype="fasta" value="eXpress_Trinity.fasta"/>
+            
+            <output name="params" file="eXpress_params.xprs" />
+            <output name="results" file="eXpress_results.xprs"/>
+        </test>
+    </tests>
+    <help>
+**eXpress Overview**
+
+eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.
+
+.. _Ensembl: http://bio.math.berkeley.edu/eXpress/
+
+-----
+
+**Input format**
+
+eXpress requires two input files:
+
+- A multi-FASTA file containing the transcript sequences.
+- Read alignments to the multi-FASTA file in BAM format.
+
+------
+
+**Outputs**
+
+- The output for eXpress is saved in a file called results.xprs in an easy-to-parse tab-delimited format.
+
+- Also, params.xprs contains the values of the other parameters (besides abundances and counts) estimated by eXpress. 
+    </help>
+</tool>
\ No newline at end of file