Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

changeset 28:c81aa97acf65 draft

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Uploaded
author jackcurragh
date Tue, 30 Aug 2022 10:54:24 +0000
parents a6b6e48756f9
children 190fa66855a8
files get_chrom_sizes/get_chrom_sizes.xml
diffstat 1 files changed, 3 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/get_chrom_sizes/get_chrom_sizes.xml	Tue Aug 30 10:12:12 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Tue Aug 30 10:54:24 2022 +0000
@@ -1,16 +1,15 @@
-<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.3">
+<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.4">
     <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description>
     <command>
-        python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2}
+        <!-- python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2}
             #if $refGenomeSource.genomeSource == "builtin":
                 none ${refGenomeSource.input1_builtin.fields.path} ${output1}
             #else:
                 ${refGenomeSource.input1_file} none ${output1}
-            #end if
+            #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