Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
changeset 41:b117f4993539 draft
Uploaded
| author | jackcurragh |
|---|---|
| date | Fri, 10 Feb 2023 12:40:31 +0000 |
| parents | 9b2bb994fc76 |
| children | 557ff294edfa |
| files | get_chrom_sizes/get_chrom_sizes.xml |
| diffstat | 1 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/get_chrom_sizes/get_chrom_sizes.xml Fri Feb 10 12:20:56 2023 +0000 +++ b/get_chrom_sizes/get_chrom_sizes.xml Fri Feb 10 12:40:31 2023 +0000 @@ -1,11 +1,15 @@ -<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.1"> +<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.2"> <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description> + <requirement type="package" version="1.13">samtools</requirement> + <command> #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 + samtools index ${refGenomeSource.input1_builtin.fields.path} + cut -f 1,2 ${refGenomeSource.input1_builtin.fields.path}.fai > $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 + samtools index ${refGenomeSource.input1_file} + cut -f 1,2 ${refGenomeSource.input1_file}.fai > $output1 #end if </command>