Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

changeset 41:b117f4993539 draft

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Uploaded
author jackcurragh
date Fri, 10 Feb 2023 12:40:31 +0000
parents 9b2bb994fc76
children 557ff294edfa
files get_chrom_sizes/get_chrom_sizes.xml
diffstat 1 files changed, 7 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/get_chrom_sizes/get_chrom_sizes.xml	Fri Feb 10 12:20:56 2023 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Fri Feb 10 12:40:31 2023 +0000
@@ -1,11 +1,15 @@
-<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.1">
+<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.2">
     <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description>
+    <requirement type="package" version="1.13">samtools</requirement>
+
     <command>
 
         #if $refGenomeSource.genomeSource == "builtin":
-            cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
+            samtools index ${refGenomeSource.input1_builtin.fields.path}
+            cut -f 1,2 ${refGenomeSource.input1_builtin.fields.path}.fai > $output1
         #else:
-            cat ${refGenomeSource.input1_file} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
+            samtools index ${refGenomeSource.input1_file}
+            cut -f 1,2 ${refGenomeSource.input1_file}.fai > $output1
         #end if
 
     </command>