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diff mauve.xml @ 1:bfe0d989004d draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:54:26 +0000
parents
children 687d2b3d29b8
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mauve.xml	Mon Jun 05 02:54:26 2023 +0000
@@ -0,0 +1,68 @@
+<tool id="edu.tamu.cpt.comparative.mauve" name="X-Vis" version="1.0" profile="16.04">
+    <description>from XMFA file</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>cpt-macros.xml</import>
+    </macros>
+    <configfiles>
+        <configfile name="index">
+		<![CDATA[
+#if ($frameHeight > 0):
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, height=$frameHeight, initial-scale=1">
+    <meta name="description" content="X-Vis">
+    <title>X-Vis</title>
+    <link rel="shortcut icon" href="favicon.ico">
+</head>
+<body>
+    <script src="mauve.js"></script>
+</body>
+</html>
+#else:
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <meta name="description" content="X-Vis">
+    <title>X-Vis</title>
+    <link rel="shortcut icon" href="favicon.ico">
+</head>
+<body>
+    <script src="mauve.js"></script>
+</body>
+</html>
+#end if
+		]]>
+		</configfile>
+    </configfiles>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+@GENOME_SELECTOR_PRE@
+mkdir -p "$output.files_path";
+
+python '$__tool_directory__/xmfa_process.py'
+@INPUT_GFF@
+@INPUT_FASTA@
+@XMFA_INPUT@
+"out" > "$output.files_path/data.json";
+mv out "$output.files_path/";
+
+cp '$__tool_directory__/mauve.js' '$output.files_path/';
+cp '$index' "$output"
+]]></command>
+    <inputs>
+        <expand macro="input/gff3+fasta"/>
+        <expand macro="xmfa_input"/>
+        <param label="Manually Set Height (0 for auto-scaling)" name="frameHeight" type="integer" value="0"/>
+    </inputs>
+    <outputs>
+        <data format="html" name="output"/>
+    </outputs>
+    <help>
+	</help>
+    <tests/>
+</tool>