Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
diff get_chrom_sizes/get_chrom_sizes.xml @ 4:c6a297d05c8e draft
Uploaded
author | jackcurragh |
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date | Fri, 13 May 2022 09:17:14 +0000 |
parents | cfdf764b9226 |
children | ec8651ac3d61 |
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--- a/get_chrom_sizes/get_chrom_sizes.xml Thu Apr 21 10:39:18 2022 +0000 +++ b/get_chrom_sizes/get_chrom_sizes.xml Fri May 13 09:17:14 2022 +0000 @@ -1,11 +1,31 @@ -<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.0"> +<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.1"> <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> <command> python $__tool_directory__/calculating_chrom.sizes.py ${input1} ${input2} ${output1} </command> <inputs> - <param name="input1" type="data" format="fasta" label="FASTA File" /> - <param name="input2" type="text" label="Chromosome Column Prefix (eg. chr)" /> + <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" type="select" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team"> + <options from_data_table="builtin_fastas"> + <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" type="data" format="fasta" label="FASTA File" /> + </when> + </conditional> + <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)"> + <option value="chr">'chr' (required for upload to GWIPS-Viz)</option> + <option value="none" selected='true'>None - do not add a prefix</option> + <option value="manual">Specify you own</option> + </param> </inputs> <outputs> @@ -21,7 +41,7 @@ <help> **What it does** -creates a chromosome sizes file from a fasta file +Creates a chromosome sizes file from a fasta file. </help> <citations/> </tool>