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+++ b/fastq_dump_paired.xml	Mon Sep 28 12:53:10 2015 -0400
@@ -0,0 +1,51 @@
+<tool id="fastq_dump_paired" name="FASTQ Dump paired downloader" version="1.0">
+    <description>Downloads a set of paired reads by their accession number using fastq-dump tool from sra-toolkit.</description>
+    <requirements>
+       <!-- Should just use the samtools that's installed in the path -->
+       <requirement type="binary">fastq-dump</requirement>
+    </requirements>
+    <command>
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+## ! We only have a simple single command here.
+fastq-dump --log-level fatal --split-3 --accession ${accession_number};
+ls -lh | grep ${accession_number};
+mv -v ${accession_number}_1.fastq R1.fastq;
+mv -v ${accession_number}_2.fastq R2.fastq;
+    </command>
+    <inputs>
+        <param name="accession_number" size="10" type="text" value="" label="Accession Number"/>
+    </inputs>
+    <outputs>
+       <data format="fastq" label="${tool.name} on ${on_string}: Forward Reads" name="forward_reads" from_work_dir="R1.fastq" >
+       </data>
+       <data format="fastq" label="${tool.name} on ${on_string}: Reverse Reads" name="reverse_reads" from_work_dir="R2.fastq" >
+       </data>
+    </outputs>
+    
+    <tests>
+    <!-- Empty -->
+    </tests>
+
+    <help>
+
+.. class:: infomark
+
+**What it does**
+
+Performs a fastq-dump with the split-3 option.
+
+::
+
+  fastq-dump --log-level fatal --split-3 --accession accession_number
+
+------
+
+.. class:: infomark
+
+**Tool Author**
+
+Mando Rodriguez
+
+    </help>
+</tool>
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