--- a/macros.xml	Fri Sep 20 04:19:02 2024 +0000
+++ b/macros.xml	Fri Sep 20 04:44:18 2024 +0000
@@ -1,31 +1,43 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2019.06.05">regex</requirement>
-            <requirement type="package" version="3.6">python</requirement>
-            <requirement type="package" version="1.77">biopython</requirement>
-            <requirement type="package" version="1.1.7">cpt_gffparser</requirement>
+            <requirement type="package" version="3.9">python</requirement>
+            <requirement type="package" version="1.81">biopython</requirement>
+            <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@BLAST_TSV@">
-		$blast_tsv
-	</token>
-    <xml name="blast_tsv">
-        <param label="Blast Results" help="TSV/tabular (25 Column)" name="blast_tsv" type="data" format="tabular"/>
+    <token name="@WRAPPER_VERSION@">2.4.0</token>
+    <xml name="citation/gepard">
+        <citation type="doi">10.1093/bioinformatics/btm039</citation>
     </xml>
-    <token name="@BLAST_XML@">
-		$blast_xml
+    <token name="@XMFA_INPUT@">
+		'$xmfa'
 	</token>
-    <xml name="blast_xml">
-        <param label="Blast Results" help="XML format" name="blast_xml" type="data" format="blastxml"/>
+    <xml name="xmfa_input" token_formats="xmfa">
+        <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
     </xml>
-    <xml name="gff3_with_fasta">
-        <param label="Genome Sequences" name="fasta" type="data" format="fasta"/>
-        <param label="Genome Annotations" name="gff3" type="data" format="gff3"/>
+    <token name="@XMFA_FA_INPUT@">
+		'$sequences'
+	</token>
+    <xml name="xmfa_fa_input">
+        <param type="data" format="fasta" name="sequences" label="Sequences in alignment" help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/>
     </xml>
     <xml name="genome_selector">
-        <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
+        <conditional name="reference_genome">
+            <param name="reference_genome_source" type="select" label="Reference Genome">
+                <option value="history" selected="True">From History</option>
+                <option value="cached">Locally Cached</option>
+            </param>
+            <when value="cached">
+                <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
+                    <options from_data_table="all_fasta"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
+            </when>
+        </conditional>
     </xml>
     <xml name="gff3_input">
         <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
@@ -34,25 +46,125 @@
         <expand macro="gff3_input"/>
         <expand macro="genome_selector"/>
     </xml>
+    <xml name="citation/mijalisrasche">
+        <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+        <citation type="bibtex">@unpublished{galaxyTools,
+		author = {E. Mijalis, H. Rasche},
+		title = {CPT Galaxy Tools},
+		year = {2013-2017},
+		note = {https://github.com/tamu-cpt/galaxy-tools/}
+		}
+		</citation>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+            <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {E. Mijalis, H. Rasche},
+				title = {CPT Galaxy Tools},
+				year = {2013-2017},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+			</citation>
+            <yield/>
+        </citations>
+    </xml>
+    <xml name="citations-crr">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+            <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {C. Ross},
+				title = {CPT Galaxy Tools},
+				year = {2020-},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+			</citation>
+            <yield/>
+        </citations>
+    </xml>
+    <xml name="citations-2020">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+            <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {E. Mijalis, H. Rasche},
+				title = {CPT Galaxy Tools},
+				year = {2013-2017},
+				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>
+            <yield/>
+        </citations>
+    </xml>
+    <xml name="citations-2020-AJC-solo">
+        <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>
+            <yield/>
+        </citations>
+    </xml>
+    <xml name="citations-clm">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+            <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {C. Maughmer},
+				title = {CPT Galaxy Tools},
+				year = {2017-2020},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+			</citation>
+            <yield/>
+        </citations>
+    </xml>
+    <xml name="sl-citations-clm">
+        <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {C. Maughmer},
+				title = {CPT Galaxy Tools},
+				year = {2017-2020},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+			</citation>
+        <yield/>
+    </xml>
     <token name="@INPUT_GFF@">
-	    $gff3_data
+	    '$gff3_data'
 	</token>
     <token name="@INPUT_FASTA@">
-		genomeref.fa
+    #if str($reference_genome.reference_genome_source) == 'cached':
+            '${reference_genome.fasta_indexes.fields.path}'
+    #else if str($reference_genome.reference_genome_source) == 'history':
+            genomeref.fa
+    #end if
 	</token>
     <token name="@GENOME_SELECTOR_PRE@">
-		ln -s $genome_fasta genomeref.fa;
+    #if $reference_genome.reference_genome_source == 'history':
+            ln -s '$reference_genome.genome_fasta' genomeref.fa;
+    #end if
 	</token>
     <token name="@GENOME_SELECTOR@">
-		genomeref.fa
+    #if str($reference_genome.reference_genome_source) == 'cached':
+            '${reference_genome.fasta_indexes.fields.path}'
+    #else if str($reference_genome.reference_genome_source) == 'history':
+            genomeref.fa
+    #end if
 	</token>
-    <xml name="input/fasta">
-        <param label="Fasta file" name="sequences" type="data" format="fasta"/>
-    </xml>
-    <token name="@SEQUENCE@">
-		$sequences
-	</token>
-    <xml name="input/fasta/protein">
-        <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
-    </xml>
 </macros>