--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chimerascan.xml	Thu Sep 07 17:55:18 2017 -0400
@@ -0,0 +1,54 @@
+<tool id="chimerascan" name="ChimeraScan">
+    <description>A tool for identifying chimeric transcription in sequencing data.</description>
+    <command detect_errors="exit_code" interpreter="python">
+            $__tool_directory__/chimerascan_run.py -p 8 $__tool_directory__/myindex 
+            #if $input_type_conditional.chimerascan_input_type == "paired"
+                    $input_type_conditional.input_1 $input_type_conditional.input_2
+            #else
+                    $input_type_conditional.input.forward $input_type_conditional.input.reverse
+            #end if
+            $galaxy_output
+    </command>
+    <inputs>
+        <conditional name="input_type_conditional">
+            <param name="chimerascan_input_type" type="select" label="Input Type" help="Select between paired and paired collection">
+                    <option value="paired" selected="true">Paired</option>
+                    <option value="paired_collection">Paired Collection</option>
+            </param>
+            <when value="paired">
+                    <param format='fastq' name='input_1' type='data' label='FASTQ file, forward reads' />
+                    <param format='fastq' name='input_2' type='data' label='FASTQ file, reverse reads' />
+            </when>
+            <when value="paired_collection">
+                    <param format="fastq" name='input' type="data_collection" collection_type="paired" label="Select a paired collection" help="Specify paired dataset collection containing paired reads"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="galaxy_output" format="bed" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input1" value="input1.fastq"/>
+            <param name="input2" value="input2.fastq"/>
+            <output name="galaxy_output" file="outputfile.bed" ftype="bed"/>
+        </test>
+        <test>
+            <param name="fastq_input">
+              <collection type="paired">
+                <element name="forward" value="input1.fastq" />
+                <element name="reverse" value="input2.fastq" />
+              </collection>
+            </param>
+            <param name="input_type" value="paired_collection" />
+            <output name="galaxy_output" file="outputfile.bed" ftype="bed"/>
+        </test>
+    </tests>
+
+    <help>
+	Bowtie index files must be placed inside 'myindex folder'
+        A tool for identifying chimeric transcription in sequencing data.
+    </help>
+
+</tool>