Mercurial > repos > triasteran > ribogalaxy_get_chrom_sizes_upd
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_chrom_sizes/get_chrom_sizes.xml Mon Feb 13 15:49:26 2023 +0000 @@ -0,0 +1,54 @@ +<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.3a"> + <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description> + <requirement type="package" version="0.7.1">pyfaidx</requirement> + + <command> + + #if $refGenomeSource.genomeSource == "builtin": + faidx ${refGenomeSource.input1_builtin.fields.path} -i chromsizes > $output1 + #else: + faidx ${refGenomeSource.input1_file} -i chromsizes > $output1 + #end if + + </command> + <inputs> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?"> + <option value="builtin">Use a built-in FASTA</option> + <option value="history">Use one from the history</option> + </param> + <when value="builtin"> + <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team"> + <options from_data_table="builtin_fastas_3"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No built-ins are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="input1_file" type="data" format="fasta" label="FASTA File" /> + </when> + </conditional> + + <param name="input2" type="text" label="Chromosome Column Prefix (add chr if absent from FASTA file for GWIPS upload)" /> + + </inputs> + <outputs> + <data name="output1" format="tabular"/> + </outputs> + <tests> + <test> + <param name="input1" value="test.fasta" ftype="fasta" /> + <param name="input2" value="chr"/> + <output name="output1" file="test.fasta.sizes" ftype="tabular" lines_diff="4" /> + </test> + </tests> + <help> +**What it does** + +Creates a chromosome sizes file from a fasta file. This is needed for creating ribosome profiles. + +Some commonly used genomes are provided to save on storage. + </help> + <citations/> +</tool>