--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Jun 05 02:42:28 2023 +0000
@@ -0,0 +1,74 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package">progressivemauve</requirement>
+            <!--<requirement type="package" version="2.7">python</requirement>-->
+            <requirement type="package" version="0.6.4">bcbiogff</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@WRAPPER_VERSION@">2.4.0</token>
+    <xml name="citation/progressive_mauve">
+        <citation type="doi">10.1371/journal.pone.0011147</citation>
+    </xml>
+    <xml name="citation/gepard">
+        <citation type="doi">10.1093/bioinformatics/btm039</citation>
+    </xml>
+    <token name="@XMFA_INPUT@">
+		'$xmfa'
+	</token>
+    <xml name="xmfa_input" token_formats="xmfa">
+        <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
+    </xml>
+    <token name="@XMFA_FA_INPUT@">
+		'$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">
+        <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"/>
+    </xml>
+    <xml name="input/gff3+fasta">
+        <expand macro="gff3_input"/>
+        <expand macro="genome_selector"/>
+    </xml>
+    <token name="@INPUT_GFF@">
+	    '$gff3_data'
+	</token>
+    <token name="@INPUT_FASTA@">
+    #if str($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@">
+    #if $reference_genome.reference_genome_source == 'history':
+            ln -s '$reference_genome.genome_fasta' genomeref.fa;
+    #end if
+	</token>
+    <token name="@GENOME_SELECTOR@">
+    #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>
+</macros>