Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

comparison get_chrom_sizes/get_chrom_sizes.xml @ 25:3276016ac5b3 draft

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author jackcurragh
date Wed, 18 May 2022 10:35:44 +0000
parents ca6a237895f3
children 185133c56545
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24:feeee18b0084 25:3276016ac5b3
1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.2"> 1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.2">
2 <description>Chromosome sizes are needed for the creation of ribosome profiles. This tool 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 <command> 3 <command>
4 python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2} 4 python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2}
5 #if $refGenomeSource.genomeSource == "builtin": 5 #if $refGenomeSource.genomeSource == "builtin":
6 none ${refGenomeSource.input1_builtin.fields.path} ${output1} 6 none ${refGenomeSource.input1_builtin.fields.path} ${output1}
7 #else: 7 #else:
8 ${refGenomeSource.input1_file} none ${output1} 8 ${refGenomeSource.input1_file} none ${output1}
9 #end if 9 #end if
10
11
12 </command> 10 </command>
13 <inputs> 11 <inputs>
14 <conditional name="refGenomeSource"> 12 <conditional name="refGenomeSource">
15 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?"> 13 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
16 <option value="builtin">Use a built-in FASTA</option> 14 <option value="builtin">Use a built-in FASTA</option>
46 </test> 44 </test>
47 </tests> 45 </tests>
48 <help> 46 <help>
49 **What it does** 47 **What it does**
50 48
51 Creates a chromosome sizes file from a fasta file. 49 Creates a chromosome sizes file from a fasta file. This is needed for creating ribosome profiles.
50
51 Some commonly used genomes are provided to save on storage.
52 </help> 52 </help>
53 <citations/> 53 <citations/>
54 </tool> 54 </tool>