Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

changeset 8:84664985411c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jackcurragh
date Tue, 17 May 2022 13:16:52 +0000
parents f1d2d3397870
children 8c5c2953c097
files get_chrom_sizes/calculating_chrom.sizes.py get_chrom_sizes/get_chrom_sizes.xml
diffstat 2 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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")
 
--- 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">