Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

changeset 34:d82cc435c5c8 draft

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Uploaded
author jackcurragh
date Fri, 23 Sep 2022 14:14:04 +0000
parents c75cfa968e2a
children 6932d7b12b41
files get_chrom_sizes/get_chrom_sizes.xml
diffstat 1 files changed, 3 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/get_chrom_sizes/get_chrom_sizes.xml	Fri Sep 23 14:09:06 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Fri Sep 23 14:14:04 2022 +0000
@@ -1,32 +1,11 @@
-<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.7">
+<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8">
     <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description>
     <command>
-        <!-- 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 -->
-
-        <!-- #if $refGenomeSource.genomeSource == "builtin":
-            #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:
-                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 -->
 
         #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
+            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
         #else:
-            #if ${input2} == "chr":
-                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
+            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>