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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA/ commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
author earlhaminst
date Mon, 24 Feb 2025 11:06:56 +0000
parents c388666f58e0
children
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7:b9f1bcf5ee59 8:a6c4483a02be
1 <tool id="gafa" name="Gene Align and Family Aggregator" version="0.3.0"> 1 <tool id="gafa" name="Gene Align and Family Aggregator" version="0.3.1">
2 <description>generates an SQLite database that can be visualised with Aequatus</description> 2 <description>generates an SQLite database that can be visualised with Aequatus</description>
3 <command detect_errors="exit_code"> 3 <command detect_errors="exit_code">
4 <![CDATA[ 4 <![CDATA[
5 python '$__tool_directory__/GAFA.py' 5 python '$__tool_directory__/GAFA.py'
6 #for $dataset in $treeFile: 6 #for $dataset in $treeFile:
12 -g '$genesFile' 12 -g '$genesFile'
13 -o '$outputFile' 13 -o '$outputFile'
14 ]]> 14 ]]>
15 </command> 15 </command>
16 <inputs> 16 <inputs>
17 <param name="treeFile" type="data" format="nhx" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" /> 17 <param name="treeFile" type="data" format="nhx,newick" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" />
18 <param name="alignmentFile" type="data" format="fasta" multiple="true" label="Protein alignments" help="Protein alignments in fasta_aln format generated by T-Coffee" /> 18 <param name="alignmentFile" type="data" format="fasta" multiple="true" label="Protein alignments" help="Protein alignments in fasta_aln format generated by T-Coffee" />
19 <param name="genesFile" type="data" format="sqlite" label="Gene features" help="Gene features in SQLite format generated by 'GSTF preparation' tool" /> 19 <param name="genesFile" type="data" format="sqlite" label="Gene features" help="Gene features in SQLite format generated by 'GSTF preparation' tool" />
20 </inputs> 20 </inputs>
21 <outputs> 21 <outputs>
22 <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" /> 22 <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" />
35 35
36 Aequatus is an open-source homology browser developed with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures. 36 Aequatus is an open-source homology browser developed with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures.
37 37
38 N.B.: The tool will modify the sequence identifiers found in the "Protein alignments" dataset by removing everything from the first underscore to the end of the string. 38 N.B.: The tool will modify the sequence identifiers found in the "Protein alignments" dataset by removing everything from the first underscore to the end of the string.
39 39
40 .. _Aequatus: http://aequatus.earlham.ac.uk 40 .. _Aequatus: https://github.com/TGAC/Aequatus
41 ]]> 41 ]]>
42 </help> 42 </help>
43 <citations> 43 <citations>
44 <citation type="doi">https://doi.org/10.1093/gigascience/giy005</citation>
44 </citations> 45 </citations>
45 </tool> 46 </tool>