--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trips_bam_to_sqlite/trips_bam_to_sqlite.xml	Mon Apr 04 09:48:32 2022 +0000
@@ -0,0 +1,37 @@
+<tool id="bam_to_sqlite" name="BAM to Sqlite (TRIPS-Viz)" version="1.0">
+    <description>Convert BAM file to SQLITE for TRIPS-Viz</description>
+    <requirements>
+        <requirement type="package" version="0.19.0">pysam</requirement>
+        <requirement type="package" version="2.0.0">sqlitedict</requirement>
+        <requirement type="package" version="3.37.1">sqlite</requirement>
+    </requirements>
+    <command><![CDATA[
+        python $__tool_directory__/bam_to_sqlite.py <path_to_bam_file> <path_to_organism.sqlite> <file_description (optional)> 
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="bam" label="BAM file" />
+        <param name="input2" type="data" format="sqlite" label="Path to organism SQLITE annotation file" />
+        <param name="input3" type="data" format="text" label="Description of this sample" />
+    </inputs>
+    <outputs>
+       <data name="output1" format="sqlite"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="test.bam" ftype="bam"/>
+            <param name="input2" value="test.sqlite" ftype="sqlite"/>
+            <param name="input3" value="TEST DESCRIPTION" ftype="text"/>
+            <output name="output1" file="test.bam.sqlite" ftype="sqlite" lines_diff="4" />
+        </test>
+    </tests>
+    <help>
+        **What it does**
+
+        Process your transcriptome read alignments for TRIPS-Viz 
+
+        Prerequisites: 
+        - name-sorted bam file (samtools sort -n)
+        - TRIPS-Viz annotation file in SQLITE format.
+    </help>
+    <citations/>
+</tool>