# HG changeset patch
# User jackcurragh
# Date 1652795366 0
# Node ID c7e2879bf357d97c26124a9f7eaa3930ddaa3a81
# Parent  afd11143fb675948e3226fabb5bfd2969657a27d
Uploaded

diff -r afd11143fb67 -r c7e2879bf357 get_chrom_sizes/calculating_chrom.sizes.py
--- a/get_chrom_sizes/calculating_chrom.sizes.py	Tue May 17 13:46:35 2022 +0000
+++ b/get_chrom_sizes/calculating_chrom.sizes.py	Tue May 17 13:49:26 2022 +0000
@@ -3,10 +3,11 @@
 from sys import argv
 # python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes
 fasta_source = str(argv[1])
-genome = str(argv[2])
-builtin = str(argv[3])
-prefix = str(argv[4])
-output = str(argv[5])
+prefix = str(argv[2])
+output = str(argv[3])
+genome = str(argv[4])
+builtin = str(argv[5])
+
 # genome = 'test-data/test.fasta'
 # output = "test-data/test_chrom.sizes"
 print(fasta_source, genome, builtin, prefix, output)
diff -r afd11143fb67 -r c7e2879bf357 get_chrom_sizes/get_chrom_sizes.xml
--- a/get_chrom_sizes/get_chrom_sizes.xml	Tue May 17 13:46:35 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Tue May 17 13:49:26 2022 +0000
@@ -1,13 +1,13 @@
 <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 ${refGenomeSource.genomeSource} 
+        python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2} ${output1}
             #if $refGenomeSource.genomeSource == "builtin":
                 ${refGenomeSource.input1_builtin.fields.path} 
             #else:
                 ${refGenomeSource.input1_file}
             #end if
-            ${input2} ${output1}
+            
     </command>
     <inputs>
         <conditional name="refGenomeSource">