Mercurial > repos > cpt > cpt_xmfa

<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>

    </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>
author	cpt
date	Fri, 05 Jan 2024 05:58:05 +0000
parents	bfe0d989004d
children