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comparison test-data/bam/test.xml @ 19:8f33c9fbc119 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
author iuc
date Fri, 06 Jul 2018 06:10:18 -0400
parents ff11d442feed
children 1cfc579079a6
comparison
equal deleted inserted replaced
18:836d1aa3e89a 19:8f33c9fbc119
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <root> 2 <root>
3 <metadata> 3 <metadata>
4 <gencode>11</gencode> 4 <gencode>11</gencode>
5 <genomes> 5 <genomes>
6 <genome>test-data/merlin.fa</genome> 6 <genome path="/tmp/tmpfqQZDj/files/000/dataset_2.dat">
7 <metadata>
8 <dataset id="9a22496ee796fbfc" hid="1"
9 size="171.6 KB"
10 edam_format="format_1929"
11 file_ext="fasta" />
12 <history id="fa6d20d0fb68383f"
13 user_email="test@bx.psu.edu"
14 user_id="2"
15 display_name="test_history"/>
16 <metadata
17 dbkey="hg17"
18 data_lines="2881"
19 sequences="1"
20 />
21 <tool
22 tool_id="upload1"
23 tool_version="1.1.4"
24 />
25 </metadata>
26 </genome>
7 </genomes> 27 </genomes>
8 <general> 28 <general>
9 <defaultLocation></defaultLocation> 29 <defaultLocation></defaultLocation>
10 <trackPadding>40</trackPadding> 30 <trackPadding>20</trackPadding>
31
11 <shareLink>true</shareLink> 32 <shareLink>true</shareLink>
12 <aboutDescription></aboutDescription> 33 <aboutDescription></aboutDescription>
13 <show_tracklist>true</show_tracklist> 34 <show_tracklist>true</show_tracklist>
14 <show_nav>true</show_nav> 35 <show_nav>true</show_nav>
15 <show_overview>false</show_overview> 36 <show_overview>true</show_overview>
16 <show_menu>true</show_menu> 37 <show_menu>true</show_menu>
17 <hideGenomeOptions>false</hideGenomeOptions> 38 <hideGenomeOptions>false</hideGenomeOptions>
18 </general> 39 </general>
40 <galaxyUrl>http://localhost</galaxyUrl>
19 </metadata> 41 </metadata>
20 <tracks> 42 <tracks>
21 <track cat="Default" format="pileup"> 43 <track cat="Aligned reads" format="pileup" visibility="default_off">
22 <files> 44 <files>
23 <trackFile path="test-data/bam/154.bam" ext="bam" label="Basic"/> 45 <trackFile path="/tmp/tmpfqQZDj/files/000/dataset_1.dat" ext="bam" label="merlin-sample.bam">
46 <metadata>
47 <dataset id="2891970512fa2d5a" hid="1"
48 size="12.9 KB"
49 edam_format="format_2572"
50 file_ext="bam" />
51 <history id="2891970512fa2d5a"
52 user_email="planemo@galaxyproject.org"
53 user_id="1"
54 display_name="Unnamed history"/>
55 <metadata
56 dbkey="hg17"
57 bam_index="__lt__galaxy.model.MetadataFile object at 0x7fc42c1d18d0__gt__"
58 bam_version="1.3"
59 sort_order="coordinate"
60 read_groups=""
61 reference_names="[SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc4484b3170 on: u__sq__Merlin__sq__]"
62 reference_lengths="[172788]"
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object at 7fc44857f230 on: u__sq__HD__sq__: {SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc44857f110 on: u__sq__SO__sq__: SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc44857f410 on: u__sq__coordinate__sq__, 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66 />
67 <tool
68 tool_id="upload1"
69 tool_version="1.1.4"
70 />
71 </metadata>
72 </trackFile>
24 </files> 73 </files>
74
25 <options> 75 <options>
76
26 <pileup> 77 <pileup>
27 <auto_snp>false</auto_snp> 78 <auto_snp>false</auto_snp>
28 <bam_indices> 79 <bam_indices>
29 <bam_index>test-data/bam/154.bam.bai</bam_index> 80 <bam_index>/tmp/tmpfqQZDj/files/_metadata_files/000/metadata_1.dat</bam_index>
30 </bam_indices>
31 </pileup>
32 </options>
33 </track>
34 <track cat="Default" format="pileup">
35 <files>
36 <trackFile path="test-data/bam/154.bam" ext="bam" label="Auto-SNP"/>
37 </files>
38 <options>
39 <pileup>
40 <auto_snp>true</auto_snp>
41 <bam_indices>
42 <bam_index>test-data/bam/154.bam.bai</bam_index>
43 </bam_indices> 81 </bam_indices>
44 </pileup> 82 </pileup>
45 </options> 83 </options>
46 </track> 84 </track>
47 </tracks> 85 </tracks>
86 <plugins
87 ComboTrackSelector=""
88 Bookmarks=""
89 GCContent=""
90 theme=""
91 />
48 </root> 92 </root>