--- a/create_ribosome_profile/create_ribosome_profile.xml	Thu Apr 28 12:08:08 2022 +0000
+++ b/create_ribosome_profile/create_ribosome_profile.xml	Wed May 18 11:57:34 2022 +0000
@@ -1,13 +1,34 @@
-<tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.a">
-    <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>
+<tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.1">
+    <description>Produce a sorted bed file of A-Site profiles of RPFs.</description>
     <requirements>
-        <requirement type="package" version="1.73">biopython</requirement>
+        <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} ${output1}</command>
+    <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} $refGenomeSource.genomeSource
+            #if $refGenomeSource.genomeSource == "builtin":
+                none ${refGenomeSource.input1_builtin.fields.path} ${input4} ${output1}
+            #else:
+                ${refGenomeSource.input1_file} none ${input4} ${output1}
+            #end if
+    </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="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
+            <option value="builtin">Use a built-in FASTA</option>
+            <option value="history">Use one from the history</option>
+        </param>
+        <when value="builtin">
+            <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
+                <options from_data_table="builtin_fastas">
+                    <filter type="sort_by" column="2" />
+                    <validator type="no_options" message="No built-ins are available" />
+                </options>
+            </param>
+        </when>
+        <when value="history">
+            <param name="input1_file" type="data" format="fasta" label="FASTA File" />
+        </when>
         <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>