Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff orthologs/evolmap_output.xml @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
| author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
|---|---|
| date | Tue, 11 Mar 2014 12:19:13 -0700 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/orthologs/evolmap_output.xml Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,40 @@ +<tool id="evolmap_output" name="EvolMAP Output Tool"> + <description>Modifies EvolMAP output</description> + <command interpreter="perl">output.pl $file $numDiffGenes '$speciesList' +#for $file in $fileList + ${file.treeFile} +#end for</command> + + <inputs> + <repeat name="fileList" title="Species fasta files - must be same order as original tree"> + <param name="treeFile" type="data" format="fasta" label="fasta file"/> + </repeat> + <param name="file" type="data" label="EvolMAP output file"/> + <param name="numDiffGenes" type="integer" value="1" label="Number of different species" /> + <param name="speciesList" type="text" area="true" size="3x25" label="Species tree - Must be same format as original EvolMAP run." /> + </inputs> + + <outputs> + <data from_work_dir="result.dat" format="txt"/> + </outputs> + + <help> + + http://labs.eemb.ucsb.edu/oakley/todd/ + + Modifies EvolMAP output. Must provide the original EvolMAP output and files used. + + Input preconditions: + Species fasta files - must be inputted in the same order as the original tree from the EvolMAP run + EvolMAP output file - must be from an EvolMAP run + Number of different species - the number of different species you want searched and pulled to the output file + Species tree - must be the same tree you used to get the EvolMAP output file in the original EvolMAP run + + Input file format: + FASTA (.fasta/.fa) + + Output format: + Text (txt) + </help> + +</tool>