--- a/get_chrom_sizes/calculating_chrom.sizes.py	Mon May 16 09:11:51 2022 +0000
+++ b/get_chrom_sizes/calculating_chrom.sizes.py	Tue May 17 13:02:31 2022 +0000
@@ -2,9 +2,11 @@
 # adapted from https://bioexpressblog.wordpress.com/2014/04/15/calculate-length-of-all-sequences-in-an-multi-fasta-file/
 from sys import argv
 # python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes
-genome = str(argv[1])
-prefix = str(argv[2])
-output = str(argv[3])
+fasta_source = str(argv[1])
+genome = str(argv[2])
+builtin = str(argv[3])
+prefix = str(argv[4])
+output = str(argv[5])
 # genome = 'test-data/test.fasta'
 # output = "test-data/test_chrom.sizes"
 

--- a/get_chrom_sizes/get_chrom_sizes.xml	Mon May 16 09:11:51 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Tue May 17 13:02:31 2022 +0000
@@ -1,7 +1,7 @@
 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.2">
     <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}
+        python $__tool_directory__/calculating_chrom.sizes.py ${genomeSource} ${input1_file} ${input1_builtin} ${input2} ${output1}
     </command>
     <inputs>
         <conditional name="refGenomeSource">
@@ -10,7 +10,7 @@
                 <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">
+                <param name="input1_builtin" 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" />
@@ -18,7 +18,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="input1" type="data" format="fasta" label="FASTA File" />
+                <param name="input1_file" type="data" format="fasta" label="FASTA File" />
             </when>
         </conditional>
         <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)">