# HG changeset patch
# User jackcurragh
# Date 1652795859 0
# Node ID f87a4b64e6ef7415f5d7f7457cf725d20461719d
# Parent  ab7b5928faeaab76276aff56faeef94e309948d0
Uploaded

diff -r ab7b5928faea -r f87a4b64e6ef get_chrom_sizes/calculating_chrom.sizes.py
--- a/get_chrom_sizes/calculating_chrom.sizes.py	Tue May 17 13:52:08 2022 +0000
+++ b/get_chrom_sizes/calculating_chrom.sizes.py	Tue May 17 13:57:39 2022 +0000
@@ -4,12 +4,12 @@
 # python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes
 fasta_source = str(argv[1])
 prefix = str(argv[2])
-genome = str(argv[3])
-builtin = str(argv[4])
+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)
 if fasta_source == 'builtin':
 	genome = builtin
 
diff -r ab7b5928faea -r f87a4b64e6ef get_chrom_sizes/get_chrom_sizes.xml
--- a/get_chrom_sizes/get_chrom_sizes.xml	Tue May 17 13:52:08 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Tue May 17 13:57:39 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 ${refGenomeSource.genomeSource} ${input2} ${output1}
+        python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2} "${output1}"
             #if $refGenomeSource.genomeSource == "builtin":
                 ${refGenomeSource.input1_builtin.fields.path} 
             #else: