# HG changeset patch
# User jackcurragh
# Date 1652793412 0
# Node ID 84664985411ce605ca070043c3039eff53d23315
# Parent  f1d2d3397870b7fa28de2ba30d947b134ff9c2d6
Uploaded

diff -r f1d2d3397870 -r 84664985411c get_chrom_sizes/calculating_chrom.sizes.py
--- a/get_chrom_sizes/calculating_chrom.sizes.py	Tue May 17 13:09:58 2022 +0000
+++ b/get_chrom_sizes/calculating_chrom.sizes.py	Tue May 17 13:16:52 2022 +0000
@@ -9,6 +9,9 @@
 output = 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
 
 chromSizesoutput = open(output,"w")
 
diff -r f1d2d3397870 -r 84664985411c get_chrom_sizes/get_chrom_sizes.xml
--- a/get_chrom_sizes/get_chrom_sizes.xml	Tue May 17 13:09:58 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Tue May 17 13:16:52 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} ${refGenomeSource.input1_file} ${refGenomeSource.input1_builtin} ${input2} ${output1}
+        python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${refGenomeSource.genomeSource.input1_file} ${refGenomeSource.genomeSource.input1_builtin} ${input2} ${output1}
     </command>
     <inputs>
         <conditional name="refGenomeSource">