Mercurial > repos > triasteran > ribogalaxy_get_chrom_sizes_upd
comparison get_chrom_sizes/get_chrom_sizes.xml @ 0:b93d6b2e561b draft
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author | triasteran |
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date | Mon, 13 Feb 2023 15:49:26 +0000 |
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children | f2306942d61a |
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-1:000000000000 | 0:b93d6b2e561b |
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1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.3a"> | |
2 <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description> | |
3 <requirement type="package" version="0.7.1">pyfaidx</requirement> | |
4 | |
5 <command> | |
6 | |
7 #if $refGenomeSource.genomeSource == "builtin": | |
8 faidx ${refGenomeSource.input1_builtin.fields.path} -i chromsizes > $output1 | |
9 #else: | |
10 faidx ${refGenomeSource.input1_file} -i chromsizes > $output1 | |
11 #end if | |
12 | |
13 </command> | |
14 <inputs> | |
15 <conditional name="refGenomeSource"> | |
16 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?"> | |
17 <option value="builtin">Use a built-in FASTA</option> | |
18 <option value="history">Use one from the history</option> | |
19 </param> | |
20 <when value="builtin"> | |
21 <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team"> | |
22 <options from_data_table="builtin_fastas_3"> | |
23 <filter type="sort_by" column="2" /> | |
24 <validator type="no_options" message="No built-ins are available" /> | |
25 </options> | |
26 </param> | |
27 </when> | |
28 <when value="history"> | |
29 <param name="input1_file" type="data" format="fasta" label="FASTA File" /> | |
30 </when> | |
31 </conditional> | |
32 | |
33 <param name="input2" type="text" label="Chromosome Column Prefix (add chr if absent from FASTA file for GWIPS upload)" /> | |
34 | |
35 </inputs> | |
36 <outputs> | |
37 <data name="output1" format="tabular"/> | |
38 </outputs> | |
39 <tests> | |
40 <test> | |
41 <param name="input1" value="test.fasta" ftype="fasta" /> | |
42 <param name="input2" value="chr"/> | |
43 <output name="output1" file="test.fasta.sizes" ftype="tabular" lines_diff="4" /> | |
44 </test> | |
45 </tests> | |
46 <help> | |
47 **What it does** | |
48 | |
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> | |
53 <citations/> | |
54 </tool> |