Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

changeset 43:9ed20799253d draft default tip

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Uploaded
author jackcurragh
date Fri, 10 Feb 2023 12:53:20 +0000
parents 557ff294edfa
children
files get_chrom_sizes/get_chrom_sizes.xml
diffstat 1 files changed, 4 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- 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>