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comparison test-data/bam/test.xml @ 34:9de82b4963e6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
author iuc
date Wed, 11 Sep 2019 09:40:36 -0400
parents 2bb2e07a7a21
children
comparison
equal deleted inserted replaced
33:0ae74c70b267 34:9de82b4963e6
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 path="/tmp/tmpWtvfKr/files/000/dataset_20.dat"> 6 <genome path="/tmp/tmpqkd9zdgq/files/d/3/d/dataset_d3d20b83-6a77-4e76-bb7e-3b9fe7261453.dat">
7 <metadata> 7 <metadata>
8 <dataset id="b28067233c6d9fa0" hid="1" 8 <dataset id="238993350abc9bfd" hid="1"
9 size="171.6 KB" 9 size="171.6 KB"
10 edam_format="format_1929" 10 edam_format="format_1929"
11 file_ext="fasta" /> 11 file_ext="fasta" />
12 <history id="fa6d20d0fb68383f" 12 <history id="a90a30fafe298e1e"
13 user_email="test@bx.psu.edu" 13 user_email="test@bx.psu.edu"
14 user_id="2" 14 user_id="2"
15 display_name="test_history"/> 15 display_name="test_history"/>
16 <metadata 16 <metadata
17 dbkey="?" 17 dbkey="?"
40 <galaxyUrl>http://localhost</galaxyUrl> 40 <galaxyUrl>http://localhost</galaxyUrl>
41 </metadata> 41 </metadata>
42 <tracks> 42 <tracks>
43 <track cat="Auto Coloured" format="pileup" visibility="default_off"> 43 <track cat="Auto Coloured" format="pileup" visibility="default_off">
44 <files> 44 <files>
45 <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_21.dat" ext="bam" label="merlin-sample.bam"> 45 <trackFile path="/tmp/tmpqkd9zdgq/files/6/a/0/dataset_6a00d93a-ee34-42d5-897b-9470d6c71e1f.dat" ext="bam" label="merlin-sample.bam">
46 <metadata> 46 <metadata>
47 <dataset id="c18708cec3343c17" hid="2" 47 <dataset id="adba32ec9811aba7" hid="2"
48 size="12.9 KB" 48 size="12.9 KB"
49 edam_format="format_2572" 49 edam_format="format_2572"
50 file_ext="bam" /> 50 file_ext="bam" />
51 <history id="fa6d20d0fb68383f" 51 <history id="a90a30fafe298e1e"
52 user_email="test@bx.psu.edu" 52 user_email="test@bx.psu.edu"
53 user_id="2" 53 user_id="2"
54 display_name="test_history"/> 54 display_name="test_history"/>
55 <metadata 55 <metadata
56 dbkey="?" 56 dbkey="?"
57 bam_version="1.3" 57 bam_version="1.3"
58 sort_order="coordinate" 58 sort_order="coordinate"
59 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 7f62008d8a70 on: u__sq__Merlin__sq__]" 59 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 7f3deb10ba10 on: u__sq__Merlin__sq__]"
60 reference_lengths="[172788]" 60 reference_lengths="[172788]"
61 bam_header="{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 7f62006f0a10 on: u__sq__SQ__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 7f62006f0d70 on: u__sq__LN__sq__: 172788, 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 7f62006f0f50 on: u__sq__SN__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 7f6200fe0470 on: u__sq__Merlin__sq__}], SafeStringWrapper(unicode:__lt__class 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__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 7f6200fe00b0 on: u__sq__minimap2 -a -x sr -t 1 reference.fa /net/datasrv3hs.sanbi.ac.za/datastore/cip0/software/galaxy/galaxy-ctb/galaxy/database/files/004/dataset_4697.dat__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 7f6200fe0a10 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 7f6200fe0830 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 7f6200fe0350 on: u__sq__coordinate__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 7f6200fe0e30 on: u__sq__VN__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 7f62008d10b0 on: u__sq__1.3__sq__}}"
62 columns="12" 61 columns="12"
63 column_names="[SafeStringWrapper(str:__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 7f6200e95f18 on: __sq__QNAME__sq__, SafeStringWrapper(str:__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 7f6200e958e8 on: __sq__FLAG__sq__, SafeStringWrapper(str:__lt__class 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__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 7f6200e95418 on: __sq__QUAL__sq__, SafeStringWrapper(str:__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 7f6200e95998 on: __sq__OPT__sq__]" 62 bam_index="__lt__galaxy.model.MetadataFile(1) at 0x7f3de95da7d0__gt__"
64 bam_index="__lt__galaxy.model.MetadataFile object at 0x7f6200f6d1d0__gt__"
65 /> 63 />
66 <tool 64 <tool
67 tool_id="upload1" 65 tool_id="upload1"
68 tool_version="1.1.6" 66 tool_version="1.1.6"
69 /> 67 />
76 </custom_config> 74 </custom_config>
77 75
78 <pileup> 76 <pileup>
79 <auto_snp>false</auto_snp> 77 <auto_snp>false</auto_snp>
80 <bam_indices> 78 <bam_indices>
81 <bam_index>/tmp/tmpWtvfKr/files/_metadata_files/000/metadata_1.dat</bam_index> 79 <bam_index>/tmp/tmpqkd9zdgq/files/_metadata_files/a/5/2/metadata_a520581b-e8cc-43e5-8514-3379cd5eaafb.dat</bam_index>
82 </bam_indices> 80 </bam_indices>
83 <chunkSizeLimit>5000000</chunkSizeLimit> 81 <chunkSizeLimit>5000000</chunkSizeLimit>
84 </pileup> 82 </pileup>
85 </options> 83 </options>
86 </track> 84 </track>