<tool id="edu.tamu.cpt.gff3.customGbkToGff" name="(CPT) Genbank to GFF3: " version="20.1.0.0">
  <description> CPT made Biobython-based solution</description>
  <macros>
    <import>macros.xml</import>

  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
'$__tool_directory__/gbk_to_gff3.py'
'$gbkIn'
'$makeMRNA'
'$makeGene'
--identifier "$qualID"
--fastaFile '$fastaOut'
> '$default']]></command>
  <inputs>
    <param label="GenBank file" name="gbkIn" type="data" format="genbank"/>
    <param checked="true" label="Automatically generate any missing Gene features if CDS/RBS has none" name="makeGene" type="boolean" truevalue="--makeGene" falsevalue=""/>
    <param checked="true" label="Automatically generate missing mRNA features for genes" name="makeMRNA" type="boolean" truevalue="--makeMRNA" falsevalue=""/>
    <param label="Qualifier to derive GFF ID from" name="qualID" type="text" value="locus_tag"/>
  </inputs>
  <outputs>
    <data format="gff3" hidden="false" name="default"/>
    <data format="fasta" hidden="false" name="fastaOut"/>
  </outputs>
  <tests>
  </tests>
  <help><![CDATA[
**What it does**

A Biopython-based script to convert Genbank files to GFF3. Should resolve frame shift errors and other problems caused by the old Bioperl  solution. 

Will also attempt to automatically parent RBS, CDS, and Exon features without a locus tag to an appropriate gene feature.
]]></help>
  <citations>
    <citation type="doi">10.1371/journal.pcbi.1008214</citation>
    <citation type="bibtex">
			@unpublished{galaxyTools,
				author = {A. Criscione},
				title = {CPT Galaxy Tools},
				year = {2019-2021},
				note = {https://github.com/tamu-cpt/galaxy-tools/}
			}
                        </citation>
  </citations>
</tool>