Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

comparison get_chrom_sizes/get_chrom_sizes.xml @ 43:9ed20799253d draft default tip

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author jackcurragh
date Fri, 10 Feb 2023 12:53:20 +0000
parents 557ff294edfa
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42:557ff294edfa 43:9ed20799253d
1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.2"> 1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.3">
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="1.15.1">samtools</requirement> 3 <requirement type="package" version="0.7.1">pyfaidx</requirement>
4 4
5 <command> 5 <command>
6 6
7 #if $refGenomeSource.genomeSource == "builtin": 7 #if $refGenomeSource.genomeSource == "builtin":
8 samtools index ${refGenomeSource.input1_builtin.fields.path} 8 faidx ${refGenomeSource.input1_builtin.fields.path} -i chromsizes > $output1
9 cut -f 1,2 ${refGenomeSource.input1_builtin.fields.path}.fai > $output1
10 #else: 9 #else:
11 samtools index ${refGenomeSource.input1_file} 10 faidx ${refGenomeSource.input1_file} -i chromsizes > $output1
12 cut -f 1,2 ${refGenomeSource.input1_file}.fai > $output1
13 #end if 11 #end if
14 12
15 </command> 13 </command>
16 <inputs> 14 <inputs>
17 <conditional name="refGenomeSource"> 15 <conditional name="refGenomeSource">