# HG changeset patch
# User cpt
# Date 1655470343 0
# Node ID 787ce84e8d16733855a1a71ce656effc3cdd64ee
# Parent  11665e761b339147966374178ba67a8a1f25c6d5
Uploaded

diff -r 11665e761b33 -r 787ce84e8d16 cpt_genome_editor/macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_genome_editor/macros.xml	Fri Jun 17 12:52:23 2022 +0000
@@ -0,0 +1,62 @@
+<?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">
+	    <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
+	</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@">
+		genomeref.fa
+	</token>
+	<token name="@GENOME_SELECTOR_PRE@">
+		ln -s $genome_fasta genomeref.fa;
+	</token>
+	<token name="@GENOME_SELECTOR@">
+		genomeref.fa
+	</token>
+        <xml name="input/fasta">
+		<param label="Fasta file" name="sequences" type="data" format="fasta"/>
+	</xml>
+
+	<token name="@SEQUENCE@">
+		"$sequences"
+	</token>
+	<xml name="input/fasta/protein">
+		<param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
+	</xml>
+</macros>