--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gbk_compare.xml	Mon Jun 05 02:42:47 2023 +0000
@@ -0,0 +1,90 @@
+<tool id="edu.tamu.cpt.gbk.gbk_compare" name="Compare Genbanks" version="20.1.0">
+  <description>, compare the identity of two genbank files</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>cpt-macros.xml</import>
+  </macros>
+  <requirements>
+    <requirement type="package" version="3.7">python</requirement>
+    <requirement type="package" version="1.74">biopython</requirement>
+  </requirements>
+  <command detect_errors="aggressive"><![CDATA[
+python '$__tool_directory__/gbk_compare.py'
+'$annotation_1'
+'$annotation_2'
+--match_identity_threshold '$match_identity_threshold'
+--allowed_skipped_genes '$allowed_skipped_genes'
+'$addNotes'
+-sumOut '$sumOut'
+> '$repOut']]></command>
+  <inputs>
+    <param label="First annotated genome (Genbank)" name="annotation_1" type="data" format="genbank"/>
+    <param label="Second annotated genome (Genbank)" name="annotation_2" type="data" format="genbank"/>
+    <param label="Two genes must have at least this nucleotide identity to be considerd the same (0.00 to 1.00)" name="match_identity_threshold" type="float" value="0.70" min="0.00" max="1.00"/>
+    <param label="This many missing genes are allowed when aligning the annotations (see help below)" name="allowed_skipped_genes" type="integer" value="10"/>
+    <param label="Include 'note' field in output" name="addNotes" type="boolean" truevalue="--addNotes" falsevalue=""/>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="sumOut" label="Report Summary"/>
+    <data format="tsv" name="repOut" label="Comparison Report of Two Genomes"/>
+  </outputs>
+  <tests>
+    <param name="annotation_1" value="related.gbk"/>
+    <param name="annotation_2" value="related.1-2000.gbk"/>
+    <output name="sumOut" value="gbkCompare_summaryOut.tsv"/>
+    <output name="repOut" value="gbkCompare_reportOut.tsv"/>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+This tool quantifies the changes in annotations for a genome, such as when it has been reassembled and/or reannotated. 
+The tool does a global alignment (using pairwise2 from biopython) of the annotated genes in both files. This means that 
+the input genomes must be roughly aligned at the gene level. If there are structural rearrangements, the tool will not work. 
+The original script was written by Ryan Wick from Monash University and was adapted to work on Galaxy by the CPT team.
+
+"Allowed Skipped Genes" is the number of genes that are allowed to be present in one record but not the other. Presence is 
+determined by whether a pair of genes are above the provided identity threshold. The tool will compare the CDSs in order, 
+ie the 1st CDS from Genbank 1 and the 1st CDS from the 2nd Genbank, the 2nd CDS and 2nd CDS, and so on. When a pair fails 
+to meet the identity threshhold, one of the CDSs is skipped and the comparisons will resume but offset, ie if 3rd and 3rd 
+CDS failed, then the 3rd CDS from Genbank 1 and the 4th from Genbank 2 will be checked next, and if they pass then the 
+march down the list will resume as 4th and 5th compared to each other, then 5th and 6th, and so on. If the number of these 
+offsets exceeds the allowed skip number, then it is assumed the genbanks are too different for a meaningful for comparison, 
+and the job will fail.
+
+**Input**
+
+Files *MUST* be in gebank format.
+The tool only looks at CDS features in the genome.
+
+**Output**
+
+* A tab delimited file of the results
+* Summary of the results.
+]]></help>
+  <citations>
+    <citation type="bibtex">
+      @unpublished{galaxyTools,
+      author = {R. Wick},
+      title = {CPT Galaxy Tools},
+      year = {2020},
+      note = {https://github.com/rrwick/Compare-annotations}
+      }
+    </citation>
+    <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {C. Ross},
+				title = {CPT Galaxy Tools},
+				year = {2020-},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+			</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>