# 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>