# HG changeset patch
# User jackcurragh
# Date 1663941494 0
# Node ID c1f79fd2cecd34d96ad5ea6abe0b968553f022a0
# Parent  190fa66855a803e82b50b005f20ef0940ab87b66
Uploaded

diff -r 190fa66855a8 -r c1f79fd2cecd get_chrom_sizes/get_chrom_sizes.xml
--- a/get_chrom_sizes/get_chrom_sizes.xml	Fri Sep 23 13:55:45 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Fri Sep 23 13:58:14 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.5">
+<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.6">
     <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description>
     <command>
         <!-- python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2}
@@ -13,11 +13,13 @@
                 cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf "chr" substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
             else:
                 cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
+            end if
         #else:
             if ${input2} == "chr":
                 cat ${refGenomeSource.input1_file} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf "chr" substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
             else:
                 cat ${refGenomeSource.input1_file} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
+            end if
         #end if