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change species names to tax ids #6506

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change species names to tax ids #6506

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19 changes: 11 additions & 8 deletions tools/repeatmasker/repeatmasker.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -98,18 +98,21 @@
<option value="no">No</option>
</param>
<when value="yes">
<!-- If we are using names as identifiers, this list needs to be checked with every new version with `<conda>/envs/__repeatmasker@4.1.5/share/RepeatMasker/famdb.py lineage 'danio'`
I think it is better to use tax-ids.6239
-->
<param name="species_list" type="select" label="Species">
<option value="human" selected="true">Human (Homo sapiens)</option>
<option value="rodent">Rodent (Order Rodentia)</option>
<option value="mouse">Mouse (Mus musculus)</option>
<option value="rattus">Rat (Rattus sp.)</option>
<option value="danio">Danio (zebra fish)</option>
<option value="drosophila">Fruit fly (Drosophila melanogaster)</option>
<option value="elegans">Caenorhabditis elegans (nematode)</option>
<option value="9606" selected="true">Human (Homo sapiens) (9606)</option>
<option value="9989">Rodent (Order Rodentia) (9989)</option>
<option value="10090">Mouse (Mus musculus) (10090)</option>
<option value="10114">Rat (Rattus sp.) (10114)</option>
<option value="7954">Danio (zebra fish) (7954)</option>
<option value="7215">Fruit fly (Drosophila melanogaster) (7215)</option>
<option value="6239">Caenorhabditis elegans (nematode) (6239)</option>
</param>
</when>
<when value="no">
<param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" />
<param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name, or tax ID) used to select repeats from DFam" />
</when>
</conditional>
</when>
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