Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

comparison get_chrom_sizes/get_chrom_sizes.xml @ 41:b117f4993539 draft

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author jackcurragh
date Fri, 10 Feb 2023 12:40:31 +0000
parents 9b2bb994fc76
children 557ff294edfa
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40:9b2bb994fc76 41:b117f4993539
1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.1"> 1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.2">
2 <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description> 2 <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description>
3 <requirement type="package" version="1.13">samtools</requirement>
4
3 <command> 5 <command>
4 6
5 #if $refGenomeSource.genomeSource == "builtin": 7 #if $refGenomeSource.genomeSource == "builtin":
6 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 8 samtools index ${refGenomeSource.input1_builtin.fields.path}
9 cut -f 1,2 ${refGenomeSource.input1_builtin.fields.path}.fai > $output1
7 #else: 10 #else:
8 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 11 samtools index ${refGenomeSource.input1_file}
12 cut -f 1,2 ${refGenomeSource.input1_file}.fai > $output1
9 #end if 13 #end if
10 14
11 </command> 15 </command>
12 <inputs> 16 <inputs>
13 <conditional name="refGenomeSource"> 17 <conditional name="refGenomeSource">