<tool id="phytab_prune_with_list" name="Prune PHYTAB using list">
  <description>Filters PHYTAB dataset by comparison to a text list</description>
    <command interpreter="python">
	prune_phytab_using_list.py $input1 $matchlist $tokeep > $output
    </command>
  <inputs>
    <param name="input1" type="data" format="tabular" label="PHYTAB sequence file"/>
    <param name="matchlist" type="data" format="txt" label="List to match to data file" />
    <param name="tokeep" type="select" optional="false" label="keep|discard" help="Choose whether to keep or discard matches">
      <option value="keep">Keep lines in output that match list</option>
      <option value="discard">Remove lines in output that match list</option>
    </param>
  </inputs>
  <outputs>
    <data format="tabular" name="output" label="Phytab file ${tool.name} on ${on_string}" >
    </data>
  </outputs>
  <help>

**What it does**

This tool filters a PHYTAB sequence file to remove undesired sequences based on a list provided. 

-----

**Basic Example**

The input data must be in phytab column format (fields are tab-delimited).  Column 1 is species name, C2 is genefamily, C3 unique sequence identifier, C4 is sequence:: 

  species1	gene1	uniquenameA	acgttagcgcgctatagc
  species2	gene1	uniquenameB	acgttag--cgctataaa
  species3	gene1	uniquenameC	acgttagcgcgctatagc
  species4	gene1	uniquenameD	acgttagcgcgctatagc
  species1	gene2	uniquenameE	--gttagtttgcta
  species3	gene2	uniquenameF	gtgttagtttgcta

Sequences from selected taxa, genes, or specific sequences provided on the List input will be excluded or retained (depending on the popup option selected) in the resulting PHYTAB output. 
The format of the list may consist of

taxa only::

  species1
  species4

genes only::
  
  geneA
  geneB

specific genes from select taxa (tab-delimited)::
 
  species1   geneA
  species4   geneB

(This last sort of list is produced by the tool 'Long Branch Finder'.)

Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org

**Citations**   

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
</help>
</tool>