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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:58:05 +0000
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1 <tool id="edu.tamu.cpt.comparative.mauve" name="X-Vis" version="1.0" profile="16.04">
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2 <description>from XMFA file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5
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6 </macros>
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7 <configfiles>
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8 <configfile name="index">
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9 <![CDATA[
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10 #if ($frameHeight > 0):
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11 <!DOCTYPE html>
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12 <html lang="en">
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13 <head>
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14 <meta charset="UTF-8">
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15 <meta name="viewport" content="width=device-width, height=$frameHeight, initial-scale=1">
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16 <meta name="description" content="X-Vis">
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17 <title>X-Vis</title>
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18 <link rel="shortcut icon" href="favicon.ico">
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19 </head>
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20 <body>
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21 <script src="mauve.js"></script>
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22 </body>
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23 </html>
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24 #else:
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25 <!DOCTYPE html>
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26 <html lang="en">
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27 <head>
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28 <meta charset="UTF-8">
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29 <meta name="viewport" content="width=device-width, initial-scale=1">
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30 <meta name="description" content="X-Vis">
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31 <title>X-Vis</title>
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32 <link rel="shortcut icon" href="favicon.ico">
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33 </head>
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34 <body>
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35 <script src="mauve.js"></script>
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36 </body>
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37 </html>
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38 #end if
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39 ]]>
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40 </configfile>
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41 </configfiles>
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42 <expand macro="requirements"/>
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43 <command detect_errors="aggressive"><![CDATA[
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44 @GENOME_SELECTOR_PRE@
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45 mkdir -p "$output.files_path";
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46
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47 python '$__tool_directory__/xmfa_process.py'
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48 @INPUT_GFF@
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49 @INPUT_FASTA@
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50 @XMFA_INPUT@
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51 "out" > "$output.files_path/data.json";
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52 mv out "$output.files_path/";
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53
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54 cp '$__tool_directory__/mauve.js' '$output.files_path/';
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55 cp '$index' "$output"
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56 ]]></command>
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57 <inputs>
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58 <expand macro="input/gff3+fasta"/>
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59 <expand macro="xmfa_input"/>
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60 <param label="Manually Set Height (0 for auto-scaling)" name="frameHeight" type="integer" value="0"/>
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61 </inputs>
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62 <outputs>
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63 <data format="html" name="output"/>
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64 </outputs>
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65 <help>
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66 </help>
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67 <tests/>
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68 </tool>