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comparison jbrowse.xml @ 18:836d1aa3e89a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
author iuc
date Thu, 16 Nov 2017 09:44:45 -0500
parents ff11d442feed
children 8f33c9fbc119
comparison
equal deleted inserted replaced
17:ff11d442feed 18:836d1aa3e89a
1 <tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.2"> 1 <tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3">
2 <description>genome browser</description> 2 <description>genome browser</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <version_command>python jbrowse.py --version</version_command> 8 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
9 <command><![CDATA[ 9 <command><![CDATA[
10 10
11 #if $action.action_select == "create": 11 #if $action.action_select == "create":
12 mkdir -p $output.files_path && 12 mkdir -p $output.files_path &&
13 #else: 13 #else:
17 ## Copy the XML file into the directory, mostly for debugging 17 ## Copy the XML file into the directory, mostly for debugging
18 ## but nice if users want to reproduce locally 18 ## but nice if users want to reproduce locally
19 cp $trackxml $output.files_path/galaxy.xml && 19 cp $trackxml $output.files_path/galaxy.xml &&
20 20
21 ## 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
22 python $__tool_directory__/jbrowse.py 22 python '$__tool_directory__/jbrowse.py'
23 23
24 --jbrowse \${JBROWSE_SOURCE_DIR} 24 --jbrowse \${JBROWSE_SOURCE_DIR}
25 #if str($standalone) == "Complete": 25 #if str($standalone) == "Complete":
26 --standalone 26 --standalone
27 #end if 27 #end if
71 <root> 71 <root>
72 <metadata> 72 <metadata>
73 <gencode>$gencode</gencode> 73 <gencode>$gencode</gencode>
74 <genomes> 74 <genomes>
75 #if str($reference_genome.genome_type_select) == "indexed": 75 #if str($reference_genome.genome_type_select) == "indexed":
76 <genome>${reference_genome.genomes.fields.path}</genome> 76 <genome path="${reference_genome.genomes.fields.path}">
77 <metadata />
78 </genome>s
77 #else 79 #else
78 #for $genome in $reference_genome.genomes: 80 #for $genome in $reference_genome.genomes:
79 <genome path="$genome"> 81 <genome path="$genome">
80 <metadata> 82 <metadata>
81 <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}" 83 <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"
493 type="text" 495 type="text"
494 value="" 496 value=""
495 help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')" 497 help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
496 optional="True"/> 498 optional="True"/>
497 </section> 499 </section>
498 </when> 500 </when>
501 <when value="BlastView/View/Track/CanvasFeatures" />
499 </conditional> 502 </conditional>
500 <expand macro="track_styling" /> 503 <expand macro="track_styling" />
501 <expand macro="color_selection" /> 504 <expand macro="color_selection" />
502 <expand macro="track_menu" /> 505 <expand macro="track_menu" />
503 <expand macro="track_display" /> 506 <expand macro="track_display" />
902 </repeat> 905 </repeat>
903 906
904 <param name="uglyTestingHack" value="enabled" /> 907 <param name="uglyTestingHack" value="enabled" />
905 <output name="output" file="track_config/test.xml" lines_diff="26"/> 908 <output name="output" file="track_config/test.xml" lines_diff="26"/>
906 </test> 909 </test>
910 <test>
911 <!-- data_table -->
912 <param name="reference_genome|genome_type_select" value="indexed"/>
913 <param name="reference_genome|genomes" value="merlin"/>
914 <param name="gencode" value="1" />
915 <param name="standalone" value="Data Directory" />
916 <param name="uglyTestingHack" value="enabled" />
917 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
918 </test>
907 </tests> 919 </tests>
908 <help><![CDATA[ 920 <help><![CDATA[
909 JBrowse-in-Galaxy 921 JBrowse-in-Galaxy
910 ================= 922 =================
911 923