--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_gbkToGff3.xml	Mon Jun 05 02:43:04 2023 +0000
@@ -0,0 +1,46 @@
+<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>
+    <import>cpt-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+			@unpublished{galaxyTools,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>