Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
comparison get_chrom_sizes/get_chrom_sizes.xml @ 4:c6a297d05c8e draft
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| author | jackcurragh |
|---|---|
| date | Fri, 13 May 2022 09:17:14 +0000 |
| parents | cfdf764b9226 |
| children | ec8651ac3d61 |
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| 3:cfdf764b9226 | 4:c6a297d05c8e |
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| 1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.0"> | 1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.1"> |
| 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>Chromosome sizes are needed for the creation of ribosome profiles. This tool generates a tab delimited chrom.sizes file from an inputted fasta</description> |
| 3 <command> | 3 <command> |
| 4 python $__tool_directory__/calculating_chrom.sizes.py ${input1} ${input2} ${output1} | 4 python $__tool_directory__/calculating_chrom.sizes.py ${input1} ${input2} ${output1} |
| 5 </command> | 5 </command> |
| 6 <inputs> | 6 <inputs> |
| 7 <param name="input1" type="data" format="fasta" label="FASTA File" /> | 7 <conditional name="refGenomeSource"> |
| 8 <param name="input2" type="text" label="Chromosome Column Prefix (eg. chr)" /> | 8 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?"> |
| 9 <option value="builtin">Use a built-in FASTA</option> | |
| 10 <option value="history">Use one from the history</option> | |
| 11 </param> | |
| 12 <when value="builtin"> | |
| 13 <param name="input1" type="select" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team"> | |
| 14 <options from_data_table="builtin_fastas"> | |
| 15 <filter type="sort_by" column="2" /> | |
| 16 <validator type="no_options" message="No built-ins are available" /> | |
| 17 </options> | |
| 18 </param> | |
| 19 </when> | |
| 20 <when value="history"> | |
| 21 <param name="input1" type="data" format="fasta" label="FASTA File" /> | |
| 22 </when> | |
| 23 </conditional> | |
| 24 <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)"> | |
| 25 <option value="chr">'chr' (required for upload to GWIPS-Viz)</option> | |
| 26 <option value="none" selected='true'>None - do not add a prefix</option> | |
| 27 <option value="manual">Specify you own</option> | |
| 28 </param> | |
| 9 | 29 |
| 10 </inputs> | 30 </inputs> |
| 11 <outputs> | 31 <outputs> |
| 12 <data name="output1" format="tabular"/> | 32 <data name="output1" format="tabular"/> |
| 13 </outputs> | 33 </outputs> |
| 19 </test> | 39 </test> |
| 20 </tests> | 40 </tests> |
| 21 <help> | 41 <help> |
| 22 **What it does** | 42 **What it does** |
| 23 | 43 |
| 24 creates a chromosome sizes file from a fasta file | 44 Creates a chromosome sizes file from a fasta file. |
| 25 </help> | 45 </help> |
| 26 <citations/> | 46 <citations/> |
| 27 </tool> | 47 </tool> |