Mercurial > repos > cpt > cpt_xmfa_to_table

diff cpt_convert_xmfa/macros.xml @ 0:06d8e28d0bd7 draft default tip
Uploaded
author: cpt
date: Fri, 10 Jun 2022 08:49:43 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_convert_xmfa/macros.xml	Fri Jun 10 08:49:43 2022 +0000
@@ -0,0 +1,58 @@
+<?xml version="1.0"?>
+<macros>
+	<xml name="requirements">
+		<requirements>
+			<requirement type="package">progressivemauve</requirement>
+			<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="@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">
+	    <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>
+</macros>