Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
changeset 27:a6b6e48756f9 draft
Uploaded
| author | jackcurragh |
|---|---|
| date | Tue, 30 Aug 2022 10:12:12 +0000 |
| parents | 185133c56545 |
| children | c81aa97acf65 |
| files | get_chrom_sizes/get_chrom_sizes.xml |
| diffstat | 1 files changed, 7 insertions(+), 0 deletions(-) [+] |
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--- 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">