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comparison mauve.xml @ 1:bfe0d989004d draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:54:26 +0000
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children 687d2b3d29b8
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0:b4d7351df1ff 1:bfe0d989004d
1 <tool id="edu.tamu.cpt.comparative.mauve" name="X-Vis" version="1.0" profile="16.04">
2 <description>from XMFA file</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <configfiles>
8 <configfile name="index">
9 <![CDATA[
10 #if ($frameHeight > 0):
11 <!DOCTYPE html>
12 <html lang="en">
13 <head>
14 <meta charset="UTF-8">
15 <meta name="viewport" content="width=device-width, height=$frameHeight, initial-scale=1">
16 <meta name="description" content="X-Vis">
17 <title>X-Vis</title>
18 <link rel="shortcut icon" href="favicon.ico">
19 </head>
20 <body>
21 <script src="mauve.js"></script>
22 </body>
23 </html>
24 #else:
25 <!DOCTYPE html>
26 <html lang="en">
27 <head>
28 <meta charset="UTF-8">
29 <meta name="viewport" content="width=device-width, initial-scale=1">
30 <meta name="description" content="X-Vis">
31 <title>X-Vis</title>
32 <link rel="shortcut icon" href="favicon.ico">
33 </head>
34 <body>
35 <script src="mauve.js"></script>
36 </body>
37 </html>
38 #end if
39 ]]>
40 </configfile>
41 </configfiles>
42 <expand macro="requirements"/>
43 <command detect_errors="aggressive"><![CDATA[
44 @GENOME_SELECTOR_PRE@
45 mkdir -p "$output.files_path";
46
47 python '$__tool_directory__/xmfa_process.py'
48 @INPUT_GFF@
49 @INPUT_FASTA@
50 @XMFA_INPUT@
51 "out" > "$output.files_path/data.json";
52 mv out "$output.files_path/";
53
54 cp '$__tool_directory__/mauve.js' '$output.files_path/';
55 cp '$index' "$output"
56 ]]></command>
57 <inputs>
58 <expand macro="input/gff3+fasta"/>
59 <expand macro="xmfa_input"/>
60 <param label="Manually Set Height (0 for auto-scaling)" name="frameHeight" type="integer" value="0"/>
61 </inputs>
62 <outputs>
63 <data format="html" name="output"/>
64 </outputs>
65 <help>
66 </help>
67 <tests/>
68 </tool>