Filter BLAST by taxid #36
Description
See email and proposed solution from Thomas Berner on the galaxy-dev list http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-June/015103.html
He suggested adding a new taxid_name.loc file, e.g.
$ more taxid_name.loc Hordeum vulgare 4513 Oryza sativa 4530 Sorghum bicolor 4558 Triticum aestivum 4565 Triticum urartu 4572 Brachypodium distachyon 15368
And new parameter,
+ <conditional name="taxon">
+ <param name="taxid_selector" type="select" label="Filter by taxon id (taxid)?">
+ <option value="no" selected="True">No filtering</option>
+ <option value="yes">Filter by user-selected taxid</option>
+ </param>
+ <when value="yes">
+ <repeat name="multitax" title="taxid" min="1">
+ <param name="taxid" label="taxid" type="select">
+ <options from_file="taxid_name.loc">
+ <column name="name" index="0"/>
+ <column name="value" index="1"/>
+ </options>
+ </param>
+ <param name="exclude" label="exlude" type="boolean"/>
+ </repeat>
+ </when>
+ </conditional>with associated Cheetah syntax for the command string:
+#if $taxon.taxid_selector == "yes": + #for $r in $taxon.multitax: + #if $r.exclude: + -negative_gilist $r.taxid + #else + -window_masker_taxid "$r.taxid" + #end if + #end for +#end if
The -window_masker_taxid option seems to make sense (although may require some setup work - see http://www.ncbi.nlm.nih.gov/books/NBK1763/ for details),
-window_masker_taxid Enable WindowMasker filtering using a Taxonomic ID
However, for exclusion is it possible to give a taxid to -negative_gilist (or -gilist)?