# HG changeset patch
# User jackcurragh
# Date 1663941911 0
# Node ID cb5a2a3ed8e7806948d0c8a0e17f1db507de150a
# Parent  75df50cfe7a96bf0499e610e6d7a1ff900d2fd5d
Uploaded

diff -r 75df50cfe7a9 -r cb5a2a3ed8e7 get_chrom_sizes/get_chrom_sizes.xml
--- a/get_chrom_sizes/get_chrom_sizes.xml	Fri Sep 23 13:59:55 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Fri Sep 23 14:05:11 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.6">
+<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.7">
     <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description>
     <command>
         <!-- python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2}
@@ -9,17 +9,17 @@
             #end if -->
 
         #if $refGenomeSource.genomeSource == "builtin":
-            if ${input2} == "chr":
+            #if ${input2} == "chr":
                 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:
+            #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
+            #end if
         #else:
-            if ${input2} == "chr":
+            #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:
+            #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
         #end if
 
     </command>