--- a/get_chrom_sizes/get_chrom_sizes.xml	Thu Apr 21 10:39:18 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Fri May 13 09:17:14 2022 +0000
@@ -1,11 +1,31 @@
-<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.0">
+<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.1">
     <description>Chromosome sizes are needed for the creation of ribosome profiles. This tool generates a tab delimited chrom.sizes file from an inputted fasta</description>
     <command>
         python $__tool_directory__/calculating_chrom.sizes.py ${input1} ${input2} ${output1}
     </command>
     <inputs>
-        <param name="input1" type="data" format="fasta" label="FASTA File" />
-        <param name="input2" type="text" label="Chromosome Column Prefix (eg. chr)" />
+        <conditional name="refGenomeSource">
+            <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" type="select" 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" type="data" format="fasta" label="FASTA File" />
+            </when>
+        </conditional>
+        <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)">
+            <option value="chr">'chr' (required for upload to GWIPS-Viz)</option>
+            <option value="none" selected='true'>None - do not add a prefix</option>
+            <option value="manual">Specify you own</option> 
+        </param> 
 
     </inputs>
     <outputs>
@@ -21,7 +41,7 @@
     <help>
 **What it does**
 
-creates a chromosome sizes file from a fasta file
+Creates a chromosome sizes file from a fasta file. 
     </help>
     <citations/>
 </tool>