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view cpt_xmfa/mauve.xml @ 0:b4d7351df1ff draft

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author cpt
date Tue, 05 Jul 2022 05:07:32 +0000
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<?xml version="1.0"?>
<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>