# HG changeset patch
# User ulfschaefer
# Date 1467987065 14400
# Node ID c1d07a00651a9ee839994f6ba0255974f359f0a0
# Parent  d85171c5a77628563fea94d734c15a30ffe8999d
Uploaded

diff -r d85171c5a776 -r c1d07a00651a MOST.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MOST.xml	Fri Jul 08 10:11:05 2016 -0400
@@ -0,0 +1,49 @@
+<tool id="most" name="MOST">
+	<description>Determine MLST from sequencing reads</description>
+
+    <requirements>
+        <requirement type="package" version="2.7.10">python</requirement>
+        <requirement type="package" version="3.2.3">lxml</requirement>
+        <requirement type="package" version="3.11">pyyaml</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="1.66">biopython</requirement>
+        <requirement type="package" version="2.1.0">bowtie2</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="5.0.0">emboss</requirement>
+        <requirement type="package" version="2.2.27">blast_plus</requirement>
+        <requirement type="package" version="1.0">phemost</requirement>
+    </requirements>
+
+	<command interpreter="bash">
+	MOST.sh
+	$fwd_file
+	$rev_file
+	$out1
+	$out2
+	"${organism.fields.file_path}"
+	</command>
+
+	<inputs>
+        <param name="fwd_file" type="data" format="fastq" label="Read dataset for direction 1" help="Select fastq R1 here."/>
+        <param name="rev_file" type="data" format="fastq" label="Read dataset for direction 2" help="Select fastq R2 here."/>
+        <param name="organism" type="select" label="Select an organism">
+            <options from_data_table="mlst_data">
+                <column name="value" index="0"/>
+                <column name="dbkey" index="1"/>
+                <column name="name" index="2"/>
+                <column name="time_stamp" index="3"/>
+                <column name="file_path" index="4"/>
+                <validator type="no_options" message="No indexes are available" />
+            </options>
+        </param>
+	</inputs>
+
+	<outputs>
+	    <data name="out1" format="xml" label="${fwd_file.name}: MLST result XML"/>
+	    <data name="out2" format="csv" label="${fwd_file.name}: MLST result CSV"/>
+	</outputs>
+
+	<help>
+		https://github.com/phe-bioinformatics/MOST
+	</help>
+</tool>