Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
changeset 32:cb5a2a3ed8e7 draft
Uploaded
| author | jackcurragh |
|---|---|
| date | Fri, 23 Sep 2022 14:05:11 +0000 |
| parents | 75df50cfe7a9 |
| children | c75cfa968e2a |
| files | get_chrom_sizes/get_chrom_sizes.xml |
| diffstat | 1 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- 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>