Mercurial > repos > iuc > jbrowse
diff test-data/bam/test.xml @ 19:8f33c9fbc119 draft
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 |
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--- a/test-data/bam/test.xml Thu Nov 16 09:44:45 2017 -0500 +++ b/test-data/bam/test.xml Fri Jul 06 06:10:18 2018 -0400 @@ -3,46 +3,90 @@ <metadata> <gencode>11</gencode> <genomes> - <genome>test-data/merlin.fa</genome> + <genome path="/tmp/tmpfqQZDj/files/000/dataset_2.dat"> + <metadata> + <dataset id="9a22496ee796fbfc" hid="1" + size="171.6 KB" + edam_format="format_1929" + file_ext="fasta" /> + <history id="fa6d20d0fb68383f" + user_email="test@bx.psu.edu" + user_id="2" + display_name="test_history"/> + <metadata + dbkey="hg17" + data_lines="2881" + sequences="1" + /> + <tool + tool_id="upload1" + tool_version="1.1.4" + /> + </metadata> + </genome> </genomes> <general> <defaultLocation></defaultLocation> - <trackPadding>40</trackPadding> + <trackPadding>20</trackPadding> + <shareLink>true</shareLink> <aboutDescription></aboutDescription> <show_tracklist>true</show_tracklist> <show_nav>true</show_nav> - <show_overview>false</show_overview> + <show_overview>true</show_overview> <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> + <galaxyUrl>http://localhost</galaxyUrl> </metadata> <tracks> - <track cat="Default" format="pileup"> + <track cat="Aligned reads" format="pileup" visibility="default_off"> <files> - <trackFile path="test-data/bam/154.bam" ext="bam" label="Basic"/> + <trackFile path="/tmp/tmpfqQZDj/files/000/dataset_1.dat" ext="bam" label="merlin-sample.bam"> + <metadata> + <dataset id="2891970512fa2d5a" hid="1" + size="12.9 KB" + edam_format="format_2572" + file_ext="bam" /> + <history id="2891970512fa2d5a" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Unnamed history"/> + <metadata + dbkey="hg17" + bam_index="__lt__galaxy.model.MetadataFile object at 0x7fc42c1d18d0__gt__" + bam_version="1.3" + sort_order="coordinate" + read_groups="" + 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__]" + reference_lengths="[172788]" + 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 7fc44857fb90 on: u__sq__SQ__sq__: [{SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class 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<bam_index>/tmp/tmpfqQZDj/files/_metadata_files/000/metadata_1.dat</bam_index> </bam_indices> </pileup> </options> </track> </tracks> -</root> + <plugins + ComboTrackSelector="" + Bookmarks="" + GCContent="" + theme="" + /> +</root> \ No newline at end of file