# HG changeset patch
# User jackcurragh
# Date 1661854332 0
# Node ID a6b6e48756f94c3c5f7237213559ba861b3b634e
# Parent  185133c565458bb68e1cbd5628e9f2042feffa8a
Uploaded

diff -r 185133c56545 -r a6b6e48756f9 get_chrom_sizes/get_chrom_sizes.xml
--- a/get_chrom_sizes/get_chrom_sizes.xml	Fri May 27 10:13:03 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Tue Aug 30 10:12:12 2022 +0000
@@ -7,6 +7,13 @@
             #else:
                 ${refGenomeSource.input1_file} none ${output1}
             #end if
+
+        #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
+            none ${refGenomeSource.input1_builtin.fields.path} ${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
+        #end if
     </command>
     <inputs>
         <conditional name="refGenomeSource">