Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
comparison get_chrom_sizes/get_chrom_sizes.xml @ 43:9ed20799253d draft default tip
Uploaded
author | jackcurragh |
---|---|
date | Fri, 10 Feb 2023 12:53:20 +0000 |
parents | 557ff294edfa |
children |
comparison
equal
deleted
inserted
replaced
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"> |