--- a/cpt_genome_editor/macros.xml	Fri Jun 17 12:48:06 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
-<?xml version="1.0"?>
-<macros>
-	<xml name="requirements">
-		<requirements>
-			<requirement type="package" version="3.8.13">python</requirement>
-			<requirement type="package" version="1.79">biopython</requirement>
-			<requirement type="package" version="1.2.2">cpt_gffparser</requirement>  
-			<yield/>
-		</requirements>
-	</xml>
-	<token name="@BLAST_TSV@">
-		"$blast_tsv"
-	</token>
-	<xml name="blast_tsv">
-		<param label="Blast Results" help="TSV/tabular (25 Column)"
-			name="blast_tsv" type="data" format="tabular" />
-	</xml>
-
-	<token name="@BLAST_XML@">
-		"$blast_xml"
-	</token>
-	<xml name="blast_xml">
-		<param label="Blast Results" help="XML format"
-			name="blast_xml" type="data" format="blastxml" />
-	</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" />
-	</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>
-        <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>