--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/retrieve.xml	Mon Jan 22 16:41:50 2018 -0500
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<tool name="Retrieve" id="sbtas_se_retrieve" version="1.0.0">
+    <description>data from SRA</description>
+    <requirements>
+        <requirement type="package" version="2.7.10">python</requirement>
+        <requirement type="package" version="2.8.2">sra-tools</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+<![CDATA[
+    python '$__tool_directory__/retrieve.py'
+    #set file_paths = ','.join( [ str( $f ) for $f in $files ] )
+    --files '${file_paths}'
+    #set file_names = ','.join( [ str( $f.name ) for $f in $files ] )
+        --names '${file_names}'
+    --format '${dataformat}'
+    --appdata 'tmp'
+    > ${stdouterr}
+]]>
+    </command>
+    <inputs>
+        <param format="txt" name="files" type="data" label="Select input files" multiple="true" optional="false" help="Select one or more txt files containing a list of accession numbers." />
+        <param name="dataformat" type="select" label="Select a data format" help="Select a data format for the accession numbers related files that will be downloaded">
+            <option value=".fastq">.fastq</option>
+            <option value=".fastq.gz">.fastq.gz</option>
+            <option value=".fasta">.fasta</option>
+            <option value=".fasta.gz">.fasta.gz</option>
+        </param>
+    </inputs>
+    <outputs>
+        <collection name="list_output" type="list:list" label="${tool.name} Accessions: Output Collection">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)_(?P&lt;ext&gt;[^_]+)_(?P&lt;dbkey&gt;[^_]+)" ext="auto" visible="False" directory="tmp" />
+        </collection>
+        <data format="txt" name="stdouterr" />
+    </outputs>
+
+    <help><![CDATA[
+Authors: Fabio Cumbo, Robert S. Harris, Chen Sun
+
+This tool will retrieve fastq files associated to the accession numbers listed in the input files.
+    ]]></help>
+</tool>