<?xml version="1.0"?>
<tool id="gbtofasta" name="gbToFasta" version="1.0">
    <description>Convert GenBank records to fasta and Create table with coding regions information for each mRNA record</description>
    <requirements>
      <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    gbToFaRa
            /dev/null
            '${outputfa}'
            outputra
            outputta
            '${gbfile}'
      #if $cds == "yes"
            && raToTab
                  -cols=acc,cds
                  outputra
                  cds_file
            && python $__tool_directory__/filter.py -f cds_file -o '${outputcds}'
      #end if
]]></command>
      <inputs>
            <param type="data" name="gbfile" format="genbank" />
            <param type="select" name="cds" label="Create table with coding regions information for each mRNA record" >
                  <option value="yes">Yes</option>
                  <option value="no">No</option>
            </param>
                  
      </inputs>
      <outputs>
            <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data>
            <data format="tabular" name="outputcds" label="${tool.name} on ${on_string}:cds">
                  <filter>cds == "yes"</filter>
            </data>
      </outputs>
  <tests>
      <test>
            <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
            <param name="cds" value="yes" />
            <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
            <output name="outputcds" value="Gallus_gallus_RefSeq.cds" />
      </test>
      <test>
            <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
            <param name="cds" value="no" />
            <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
      </test>
  </tests> 
  <help>
        <![CDATA[
gbToFasta
=========

Convert GenBank records to fasta
---------------------------------

gbToFaRa - Convert GenBank flat format file to an fa file containing
the sequence data, an ra file containing other relevant info and
a ta file containing summary statistics.
usage:
   gbToFaRa filterFile faFile raFile taFile genBankFile(s)
where filterFile is definition of which records and fields
use /dev/null if you want no filtering.

gbToFaRa /dev/null gbfile.fa \
  gbfile.ra gbfile.ta gbfile

Create table with coding regions information for each mRNA record
-----------------------------------------------------------------
raToTab - Convert ra file to table.
raToTab -cols=acc,cds gbfile.ra gbfile.cds

Source code:
============

http://hgdownload.cse.ucsc.edu/admin/exe/

]]></help> 
 <citations>
            <citation type="bibtex">@article{kent2002blat,
                  title={BLAT—the BLAST-like alignment tool},
                  author={Kent, W James},
                  journal={Genome research},
                  volume={12},
                  number={4},
                  pages={656--664},
                  year={2002},
                  publisher={Cold Spring Harbor Lab}
            }</citation>
      </citations> 
      
</tool>