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comparison jbrowse.xml @ 22:5f70e7fe6077 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author iuc
date Tue, 30 Oct 2018 18:57:53 -0400
parents 1c718d8b3532
children dba3c47e1798
comparison
equal deleted inserted replaced
21:1c718d8b3532 22:5f70e7fe6077
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command> 8 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
9 <command><![CDATA[ 9 <command><![CDATA[
10
11 #if $action.action_select == "create": 10 #if $action.action_select == "create":
12 mkdir -p $output.files_path && 11 mkdir -p $output.files_path &&
13 #else: 12 #else:
14 cp -R $action.update_jbrowse.extra_files_path $output.files_path && 13 cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
15 #end if 14 #end if
33 mv $output.files_path/index.html $output; 32 mv $output.files_path/index.html $output;
34 #else: 33 #else:
35 mv $dummyIndex $output; 34 mv $dummyIndex $output;
36 #end if 35 #end if
37 36
38
39 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. 37 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
40 #if str($uglyTestingHack) == "enabled": 38 #if str($uglyTestingHack) == "enabled":
41 mv $trackxml $output 39 mv $trackxml $output
42 #end if 40 #end if
43 ]]></command> 41 ]]></command>
44 <configfiles> 42 <configfiles>
45 <configfile name="dummyIndex"> 43 <configfile name="dummyIndex"><![CDATA[
46 <![CDATA[
47 <html> 44 <html>
48 <head> 45 <head>
49 </head> 46 </head>
50 <body> 47 <body>
51 <h1>JBrowse Data Directory</h1> 48 <h1>JBrowse Data Directory</h1>
63 Convert to Standalone" tool in Galaxy to "upgrade" to a full 60 Convert to Standalone" tool in Galaxy to "upgrade" to a full
64 JBrowse instance. 61 JBrowse instance.
65 </p> 62 </p>
66 </body> 63 </body>
67 </html> 64 </html>
68 ]]> 65 ]]></configfile>
69 </configfile>
70 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> 66 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
71 <root> 67 <root>
72 <metadata> 68 <metadata>
73 <gencode>$gencode</gencode> 69 <gencode>$gencode</gencode>
74 <genomes> 70 <genomes>
343 type="data" 339 type="data"
344 multiple="True" /> 340 multiple="True" />
345 </when> 341 </when>
346 </conditional> 342 </conditional>
347 343
348 <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/> 344 <param name="standalone" type="boolean" truevalue="Complete" falsevalue="Data Directory" checked="true" label="Produce Standalone Instance" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo"/>
349 345
350 <param label="Genetic Code" name="gencode" type="select"> 346 <param name="gencode" type="select" label="Genetic Code">
351 <option value="1">1. The Standard Code</option> 347 <option value="1">1. The Standard Code</option>
352 <option value="2">2. The Vertebrate Mitochondrial Code</option> 348 <option value="2">2. The Vertebrate Mitochondrial Code</option>
353 <option value="3">3. The Yeast Mitochondrial Code</option> 349 <option value="3">3. The Yeast Mitochondrial Code</option>
354 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> 350 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
355 <option value="5">5. The Invertebrate Mitochondrial Code</option> 351 <option value="5">5. The Invertebrate Mitochondrial Code</option>
373 <option value="create">New JBrowse Instance</option> 369 <option value="create">New JBrowse Instance</option>
374 <option value="update">Update exising JBrowse Instance</option> 370 <option value="update">Update exising JBrowse Instance</option>
375 </param> 371 </param>
376 <when value="create" /> 372 <when value="create" />
377 <when value="update"> 373 <when value="update">
378 <param label="Previous JBrowse Instance" 374 <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" />
379 name="update_jbrowse"
380 type="data"
381 format="html" />
382 </when> 375 </when>
383 </conditional> 376 </conditional>
384 377
385 <repeat name="track_groups" title="Track Group"> 378 <repeat name="track_groups" title="Track Group">
386 <param label="Track Category" 379 <param label="Track Category"
1189 selector. 1182 selector.
1190 - Non GFF3 likely has issue with automatically determined min/max 1183 - Non GFF3 likely has issue with automatically determined min/max
1191 scores. Manually specify minimum and maximum score attributes, or do 1184 scores. Manually specify minimum and maximum score attributes, or do
1192 not use varied colours based on scores to avoid this issue. 1185 not use varied colours based on scores to avoid this issue.
1193 1186
1194
1195 @ATTRIBUTION@ 1187 @ATTRIBUTION@
1196 ]]></help> 1188 ]]></help>
1197 <expand macro="citations"/> 1189 <expand macro="citations"/>
1198 </tool> 1190 </tool>