--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_ribosome_profile/create_ribosome_profile.xml	Mon Apr 04 09:58:52 2022 +0000
@@ -0,0 +1,36 @@
+<tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.0">
+    <description>Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.</description>
+    <requirements>
+        <requirement type="package" version="1.79">biopython</requirement>
+        <requirement type="package" version="0.19.0">pysam</requirement>
+    </requirements>
+    <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} ${input3} ${input4}</command>
+    <inputs>
+        <param name="input1" type="data" format="bam" label="BAM file to process"/>
+        <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
+        <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/>
+        <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase">
+            <option value="offset" selected="true">Use offset approach</option>
+            <option value="weight">Use weight centered approach</option>
+        </param>
+    </inputs>
+    <outputs>
+       <data name="output1" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="test.bam.sorted"/>
+            <param name="input2" value="15"/>
+            <param name="input3" value="sacCer3_transcripts.fasta"/>
+            <param name="input4" value="offset"/>
+            <output name="output1" file="test.bam.sorted.bed.sorted " ftype="tabular" lines_diff="4" />
+        </test>
+    </tests>
+    <help>
+    **What it does**
+
+    Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.
+
+    </help>
+    <citations/>
+</tool>