<tool id="fasta_concatenate" name="FASTA Concatenate" version="1.0">
  <description>FASTA alignment by species</description>
  <command interpreter="python">fasta_concatenate_by_species.py $input1 $out_file1</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="FASTA alignment"/>
  </inputs>
  <outputs>
    <data name="out_file1" format="fasta"/>
  </outputs>
  <tests>
    <test>
      <param name="input1" value="cf_maf2fasta.dat" />
      <output name="out_file1" file="fasta_concatenate_out.fasta" />
    </test>
  </tests>
  <help>
**What it does**
  
This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment.
It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species.

-------

**Example**

Starting FASTA::
  
  >hg18.chr1(+):10016339-10016341|hg18_0
  GT
  >panTro2.chr1(+):10195380-10195382|panTro2_0
  GT
  >rheMac2.chr1(+):13119747-13119749|rheMac2_0
  GT
  >mm8.chr4(-):148269679-148269681|mm8_0
  GT
  >canFam2.chr5(+):66213635-66213637|canFam2_0
  GT
  
  >hg18.chr1(-):100323677-100323679|hg18_1
  GT
  >panTro2.chr1(-):101678671-101678673|panTro2_1
  GT
  >rheMac2.chr1(-):103154011-103154013|rheMac2_1
  GT
  >mm8.chr3(+):116620616-116620618|mm8_1
  GT
  >canFam2.chr6(+):52954092-52954094|canFam2_1
  GT
  


becomes::
  
  >hg18
  GTGT
  >panTro2
  GTGT
  >rheMac2
  GTGT
  >mm8
  GTGT
  >canFam2
  GTGT


.. class:: warningmark 

 This tool will only work properly on files with Galaxy style FASTA headers.

-------

**Additional Information**

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>