Mercurial > repos > cpt > cpt_find_spanins

diff macros.xml @ 3:fd70980a516b draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author: cpt
date: Mon, 05 Jun 2023 02:42:01 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Jun 05 02:42:01 2023 +0000
@@ -0,0 +1,58 @@
+<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>
+            <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>