--- a/chimerascan.xml	Wed Sep 13 15:11:27 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<tool id="chimerascan" name="ChimeraScan">
-    <description>A tool for identifying chimeric transcription in sequencing data.</description>
-    <command detect_errors="exit_code"><![CDATA[
-            bash $__tool_directory__/run.sh $__tool_directory__ &&
-            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>