Mercurial > repos > iuc > jbrowse

comparison jbrowse.xml @ 35:3235aeb45c22 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
author iuc
date Wed, 18 Dec 2019 10:46:52 -0500
parents 9de82b4963e6
children 7ed0827da5a8
comparison
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34:9de82b4963e6 35:3235aeb45c22
14 14
15 ## Copy the XML file into the directory, mostly for debugging 15 ## Copy the XML file into the directory, mostly for debugging
16 ## but nice if users want to reproduce locally 16 ## but nice if users want to reproduce locally
17 cp $trackxml $output.files_path/galaxy.xml && 17 cp $trackxml $output.files_path/galaxy.xml &&
18 18
19 export JBROWSE_SOURCE_DIR=\$(dirname \$(which prepare-refseqs.pl))/../opt/jbrowse &&
20
19 ## Once that's done, we run the python script to handle the real work 21 ## Once that's done, we run the python script to handle the real work
20 python '$__tool_directory__/jbrowse.py' 22 python '$__tool_directory__/jbrowse.py'
21 23
22 --jbrowse \${JBROWSE_SOURCE_DIR} 24 --jbrowse \${JBROWSE_SOURCE_DIR}
23 #if str($standalone) == "Complete": 25 #if str($standalone) == "Complete":
26 28
27 --outdir $output.files_path 29 --outdir $output.files_path
28 $trackxml && 30 $trackxml &&
29 31
30 #if str($standalone) == "Complete": 32 #if str($standalone) == "Complete":
31 mv $output.files_path/index.html $output; 33 cp $output.files_path/index.html $output;
32 #else: 34 #else:
33 mv $dummyIndex $output; 35 cp $dummyIndex $output;
34 #end if 36 #end if
35 37
36 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. 38 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
37 #if str($uglyTestingHack) == "enabled": 39 #if str($uglyTestingHack) == "enabled":
38 mv $trackxml $output 40 cp $trackxml $output
39 #end if 41 #end if
40 ]]></command> 42 ]]></command>
41 <configfiles> 43 <configfiles>
42 <configfile name="dummyIndex"><![CDATA[ 44 <configfile name="dummyIndex"><![CDATA[
43 <html> 45 <html>