# HG changeset patch
# User jackcurragh
# Date 1676033600 0
# Node ID 9ed20799253dc1b0a916879778e2eba52c1b1f9b
# Parent  557ff294edfa6a77ecf9d833e8fbb4a34ccba9f0
Uploaded

diff -r 557ff294edfa -r 9ed20799253d get_chrom_sizes/get_chrom_sizes.xml
--- a/get_chrom_sizes/get_chrom_sizes.xml	Fri Feb 10 12:46:21 2023 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Fri Feb 10 12:53:20 2023 +0000
@@ -1,15 +1,13 @@
-<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.2">
+<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.3">
     <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description>
-    <requirement type="package" version="1.15.1">samtools</requirement>
+    <requirement type="package" version="0.7.1">pyfaidx</requirement>
 
     <command>
 
         #if $refGenomeSource.genomeSource == "builtin":
-            samtools index ${refGenomeSource.input1_builtin.fields.path}
-            cut -f 1,2 ${refGenomeSource.input1_builtin.fields.path}.fai > $output1
+            faidx ${refGenomeSource.input1_builtin.fields.path} -i chromsizes > $output1
         #else:
-            samtools index ${refGenomeSource.input1_file}
-            cut -f 1,2 ${refGenomeSource.input1_file}.fai > $output1
+            faidx ${refGenomeSource.input1_file} -i chromsizes > $output1
         #end if
 
     </command>