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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA/ commit d96cd7ee9c686c185b6734aa08ab5a891cc44149-dirty
author earlhaminst
date Mon, 03 Mar 2025 17:47:53 +0000
parents a6c4483a02be
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ab5611663f32 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA/ commit d96cd7ee9c686c185b6734aa08ab5a891cc44149-dirty
earlhaminst
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1 <tool id="gafa" name="Gene Align and Family Aggregator" version="0.4.0">
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2 <description>generates an SQLite database that can be visualised with Aequatus</description>
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3 <requirements>
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4 <requirement type="package" version="3.13">python</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 python3 '$__tool_directory__/GAFA.py'
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9 #for $dataset in $treeFile:
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10 -t '$dataset'
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11 #end for
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12 #for $dataset in $alignmentFile:
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13 -a '$dataset'
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14 #end for
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15 -g '$genesFile'
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16 -o '$outputFile'
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17 ]]>
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18 </command>
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19 <inputs>
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20 <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" />
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21 <param name="alignmentFile" type="data" format="fasta" multiple="true" label="Protein alignments" help="Protein alignments in fasta_aln format generated by T-Coffee" />
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22 <param name="genesFile" type="data" format="sqlite" label="Gene features" help="Gene features in SQLite format generated by 'GSTF preparation' tool" />
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23 </inputs>
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24 <outputs>
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25 <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="treeFile" ftype="nhx" value="tree1.nhx,tree2.nhx,tree3.nhx,tree4.nhx" />
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30 <param name="alignmentFile" ftype="fasta" value="align1.fasta,align2.fasta,align3.fasta,align4.fasta" />
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31 <param name="genesFile" ftype="sqlite" value="gene.sqlite" />
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32 <output name="outputFile" file="test.gafa.sqlite" compare="sim_size" />
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33 </test>
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34 </tests>
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35 <help>
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36 <![CDATA[
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37 Simple tool to generate an SQLite database that can be visualised with `Aequatus`_.
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39 Aequatus is an open-source homology browser developed with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures.
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40
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41 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.
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42
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43 .. _Aequatus: https://github.com/TGAC/Aequatus
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44 ]]>
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45 </help>
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46 <citations>
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47 <citation type="doi">https://doi.org/10.1093/gigascience/giy005</citation>
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48 </citations>
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49 </tool>