Mercurial > repos > iuc > jbrowse
changeset 42:6cd09d7b5f37 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
| author | iuc |
|---|---|
| date | Sat, 06 Feb 2021 12:01:13 +0000 |
| parents | 8774b28235bb |
| children | 4542035c1075 |
| files | jbrowse.xml test-data/bam/test.xml test-data/bed/test.xml test-data/custom_config/test.xml test-data/endpoints/test.xml test-data/gencode/test-1.xml test-data/gencode/test-data_table.xml test-data/gencode/test.xml test-data/gff3/test.xml test-data/menus/test.xml test-data/track_config/test.xml |
| diffstat | 11 files changed, 87 insertions(+), 1474 deletions(-) [+] |
line wrap: on
line diff
--- a/jbrowse.xml Thu Dec 31 16:00:42 2020 +0000 +++ b/jbrowse.xml Sat Feb 06 12:01:13 2021 +0000 @@ -683,7 +683,17 @@ <param name="gencode" value="1" /> <param name="standalone" value="data" /> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gencode/test-1.xml" lines_diff="16"/> + <output name="output"> + <assert_contents> + <has_text text="<gencode>1</gencode>"></has_text> + <has_text text="genome path="></has_text> + <has_text text="dataset id="></has_text> + <has_text text="history id="></has_text> + <has_text text="metadata"></has_text> + <has_text text="tool_id"></has_text> + + </assert_contents> + </output> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -691,7 +701,16 @@ <param name="gencode" value="11" /> <param name="standalone" value="data" /> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gencode/test.xml" lines_diff="16"/> + <output name="output"> + <assert_contents> + <has_text text="<gencode>11</gencode>"></has_text> + <has_text text="genome path="></has_text> + <has_text text="dataset id="></has_text> + <has_text text="history id="></has_text> + <has_text text="metadata"></has_text> + <has_text text="tool_id"></has_text> + </assert_contents> + </output> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -708,7 +727,19 @@ </repeat> </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="bed/test.xml" lines_diff="32"/> + <output name="output"> + <assert_contents> + <has_text text="<gencode>11</gencode>"></has_text> + <has_text text="genome path="></has_text> + <has_text text="dataset id="></has_text> + <has_text text="history id="></has_text> + <has_text text="metadata"></has_text> + <has_text text="tool_id"></has_text> + <has_text text="trackFile path="></has_text> + <has_text text="ext="bed" label="test-3.bed""></has_text> + <has_text text="NeatHTMLFeatures"></has_text> + </assert_contents> + </output> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -904,7 +935,18 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gff3/test.xml" lines_diff="260" /> + <output name="output"> + <assert_contents> + <has_text text="Auto Coloured"/> + <has_text text="A.gff"/> + <has_text text="B.gff"/> + <has_text text="C.gff"/> + <has_text text="D.gff"/> + <has_text text="Scaled Colour"/> + <has_text text="1.gff"/> + <has_text text="2.gff"/> + </assert_contents> + </output> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -967,7 +1009,14 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="menus/test.xml" lines_diff="44"/> + <output name="output"> + <assert_contents> + <has_text text="With menu or index"/> + <has_text text="Some menu item"/> + <has_text text="Frame title"/> + <has_text text="dijitIconNewTask"/> + </assert_contents> + </output> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -1005,7 +1054,13 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="track_config/test.xml" lines_diff="30"/> + <output name="output"> + <assert_contents> + <has_text text="With canvas config"></has_text> + <has_text text="<transcriptType>transcript</transcriptType>"></has_text> + <has_text text="<subParts>exon</subParts>"></has_text> + </assert_contents> + </output> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -1057,7 +1112,15 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="custom_config/test.xml" lines_diff="30"/> + <output name="output"> + <assert_contents> + <has_text text="1.gff"/> + <has_text text="collapsed"/> + <has_text text="150"/> + <has_text text="maxFeatureScreenDensity"/> + <has_text text="style.strandArrow"/> + </assert_contents> + </output> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -1076,7 +1139,13 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="bam/test.xml" lines_diff="42"/> + <output name="output"> + <assert_contents> + <has_text text="merlin-sample.bam"/> + <has_text text="sort_order="coordinate""/> + <has_text text="bam_index"/> + </assert_contents> + </output> </test> <test> @@ -1086,7 +1155,11 @@ <param name="gencode" value="1" /> <param name="standalone" value="data" /> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gencode/test-data_table.xml" lines_diff="4" /> + <output name="output"> + <assert_contents> + <has_text text="merlin.fa"/> + </assert_contents> + </output> </test> <test> @@ -1133,7 +1206,11 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="endpoints/test.xml" lines_diff="16"/> + <output name="output"> + <assert_contents> + <has_text text="http://example.org.external/sparql/"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[
--- a/test-data/bam/test.xml Thu Dec 31 16:00:42 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>11</gencode> - <genomes> - <genome path="/tmp/tmpqkd9zdgq/files/d/3/d/dataset_d3d20b83-6a77-4e76-bb7e-3b9fe7261453.dat"> - <metadata> - <dataset id="238993350abc9bfd" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="a90a30fafe298e1e" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </genome> - </genomes> - <general> - <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>true</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - <galaxyUrl>http://localhost</galaxyUrl> - </metadata> - <tracks> - <track cat="Auto Coloured" format="pileup" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/6/a/0/dataset_6a00d93a-ee34-42d5-897b-9470d6c71e1f.dat" ext="bam" label="merlin-sample.bam"> - <metadata> - <dataset id="adba32ec9811aba7" hid="2" - size="12.9 KB" - edam_format="format_2572" - file_ext="bam" /> - <history id="a90a30fafe298e1e" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - bam_version="1.3" - sort_order="coordinate" - 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__]" - reference_lengths="[172788]" - columns="12" - bam_index="__lt__galaxy.model.MetadataFile(1) at 0x7f3de95da7d0__gt__" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <custom_config> - </custom_config> - - <pileup> - <auto_snp>false</auto_snp> - <bam_indices> - <bam_index>/tmp/tmpqkd9zdgq/files/_metadata_files/a/5/2/metadata_a520581b-e8cc-43e5-8514-3379cd5eaafb.dat</bam_index> - </bam_indices> - <chunkSizeLimit>5000000</chunkSizeLimit> - </pileup> - </options> - </track> - </tracks> - <plugins - ComboTrackSelector="" - Bookmarks="" - GCContent="" - BlastView="True" - theme="" - /> -</root>
--- a/test-data/bed/test.xml Thu Dec 31 16:00:42 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,136 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>11</gencode> - <genomes> - <genome path="/tmp/tmpqkd9zdgq/files/2/3/a/dataset_23ae18d3-c882-4d06-a36e-5a061da14b2e.dat"> - <metadata> - <dataset id="7b55dbb89df8f4e5" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="54f2a3a23292eb07" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </genome> - </genomes> - <general> - <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>true</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - <galaxyUrl>http://localhost</galaxyUrl> - </metadata> - <tracks> - <track cat="Default" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/1/0/3/dataset_103bde9a-c404-441e-99fc-cfaeb674e4ef.dat" ext="bed" label="test-3.bed"> - <metadata> - <dataset id="fa6d20d0fb68383f" hid="2" - size="49 bytes" - edam_format="format_3003" - file_ext="bed" /> - <history id="54f2a3a23292eb07" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="3" - columns="3" - delimiter="__tc__" - chromCol="1" - startCol="2" - endCol="3" - viz_filter_cols="[4]" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - <trackFile path="/tmp/tmpqkd9zdgq/files/d/e/1/dataset_de110c59-5762-4148-ba67-f3571280eae6.dat" ext="bed" label="test-6.bed"> - <metadata> - <dataset id="683bc220e21425bb" hid="3" - size="180 bytes" - edam_format="format_3003" - file_ext="bed" /> - <history id="54f2a3a23292eb07" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="3" - columns="6" - delimiter="__tc__" - chromCol="1" - startCol="2" - endCol="3" - strandCol="6" - nameCol="4" - viz_filter_cols="[4]" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>false</index> - </gff> - </options> - </track> - </tracks> - <plugins - ComboTrackSelector="" - Bookmarks="" - GCContent="" - BlastView="True" - theme="" - /> -</root>
--- a/test-data/custom_config/test.xml Thu Dec 31 16:00:42 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,118 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>11</gencode> - <genomes> - <genome path="/tmp/tmpqkd9zdgq/files/1/a/7/dataset_1a77d084-9f64-48b9-802b-787e0e86c7b1.dat"> - <metadata> - <dataset id="a1e670e1ea0da54b" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="683bc220e21425bb" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </genome> - </genomes> - <general> - <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>true</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - <galaxyUrl>http://localhost</galaxyUrl> - </metadata> - <tracks> - <track cat="With custom track config" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/a/4/a/dataset_a4a9adc4-f3d3-4c05-8074-69e01ace1c78.dat" ext="gff3" label="1.gff"> - <metadata> - <dataset id="9a22496ee796fbfc" hid="2" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="683bc220e21425bb" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - <displayMode> - <text>collapsed</text> - </displayMode> - <histograms.height> - <integer>150</integer> - </histograms.height> - <maxFeatureScreenDensity> - <float>0.1</float> - </maxFeatureScreenDensity> - <style.strandArrow> - <boolean>false</boolean> - </style.strandArrow> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>false</index> - </gff> - </options> - </track> - </tracks> - <plugins - ComboTrackSelector="" - Bookmarks="" - GCContent="" - BlastView="True" - theme="" - /> -</root>
--- a/test-data/endpoints/test.xml Thu Dec 31 16:00:42 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,106 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>11</gencode> - <genomes> - <genome path="/tmp/tmpqkd9zdgq/files/9/5/5/dataset_955a2615-e4c3-4ccc-ae7b-749a589abc12.dat"> - <metadata> - <dataset id="27a22803849b1486" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="5449172d6ff5669b" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </genome> - </genomes> - <general> - <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>true</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - <galaxyUrl>http://localhost</galaxyUrl> - </metadata> - <tracks> - <track cat="External endpoints" format="rest" visibility="default_off"> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>Hit_titles</description> - <label>description</label> - <height>600px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - - <label>Rest api</label> - <rest> - <url>http://example.org.external/rest_api/</url> - </rest> - </options> - </track> - <track cat="External endpoints" format="sparql" visibility="default_off"> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>Hit_titles</description> - <label>description</label> - <height>600px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - - <label>Sparql endpoint</label> - <sparql> - <url>http://example.org.external/sparql/</url> - <query> DEFINE sql:select-option 'order' prefix rdf: __lt__http://www.w3.org/1999/02/22-rdf-syntax-ns#__gt__ select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }</query> - </sparql> - </options> - </track> - </tracks> - <plugins - ComboTrackSelector="" - Bookmarks="" - GCContent="" - BlastView="True" - theme="" - /> -</root>
--- a/test-data/gencode/test-1.xml Thu Dec 31 16:00:42 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>1</gencode> - <genomes> - <genome path="/tmp/tmpqkd9zdgq/files/3/1/2/dataset_312987c8-262b-4b83-b9b1-9e6e84c6bee0.dat"> - <metadata> - <dataset id="2891970512fa2d5a" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="2891970512fa2d5a" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </genome> - </genomes> - <general> - <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>true</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - <galaxyUrl>http://localhost</galaxyUrl> - </metadata> - <tracks> - </tracks> - <plugins - ComboTrackSelector="" - Bookmarks="" - GCContent="" - BlastView="True" - theme="" - /> -</root>
--- a/test-data/gencode/test-data_table.xml Thu Dec 31 16:00:42 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>1</gencode> - <genomes> - <genome path="/home/hxr/arbeit/tools-iuc/tools/jbrowse/test-data/merlin.fa"> - <metadata /> - </genome>s - </genomes> - <general> - <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>true</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - <galaxyUrl>http://localhost</galaxyUrl> - </metadata> - <tracks> - </tracks> - <plugins - ComboTrackSelector="" - Bookmarks="" - GCContent="" - BlastView="True" - theme="" - /> -</root>
--- a/test-data/gencode/test.xml Thu Dec 31 16:00:42 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>11</gencode> - <genomes> - <genome path="/tmp/tmpqkd9zdgq/files/8/b/1/dataset_8b116bbb-35ee-4d30-8d2d-ee31d8b49228.dat"> - <metadata> - <dataset id="54f2a3a23292eb07" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="5729865256bc2525" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </genome> - </genomes> - <general> - <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>true</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - <galaxyUrl>http://localhost</galaxyUrl> - </metadata> - <tracks> - </tracks> - <plugins - ComboTrackSelector="" - Bookmarks="" - GCContent="" - BlastView="True" - theme="" - /> -</root>
--- a/test-data/gff3/test.xml Thu Dec 31 16:00:42 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,592 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>11</gencode> - <genomes> - <genome path="/tmp/tmpqkd9zdgq/files/b/f/a/dataset_bfad32fe-cc05-405c-965c-6fe9b7a36908.dat"> - <metadata> - <dataset id="b842d972534ccb3e" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </genome> - </genomes> - <general> - <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>true</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - <galaxyUrl>http://localhost</galaxyUrl> - </metadata> - <tracks> - <track cat="Auto Coloured" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/7/6/2/dataset_7625da24-6a53-41c2-a7fc-c5c9719deccc.dat" ext="gff3" label="A.gff"> - <metadata> - <dataset id="5449172d6ff5669b" hid="2" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - <trackFile path="/tmp/tmpqkd9zdgq/files/c/f/c/dataset_cfcde690-dc99-4152-87ef-0936eb90f2ca.dat" ext="gff3" label="B.gff"> - <metadata> - <dataset id="9ce08b2254e4d5ed" hid="3" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - <trackFile path="/tmp/tmpqkd9zdgq/files/1/c/4/dataset_1c41cecd-9fc6-47b5-9f0b-b7bb73498675.dat" ext="gff3" label="C.gff"> - <metadata> - <dataset id="80b8022ff3f677b7" hid="4" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - <trackFile path="/tmp/tmpqkd9zdgq/files/5/b/3/dataset_5b33c8ff-b12b-4307-a35c-92ea8571dc04.dat" ext="gff3" label="D.gff"> - <metadata> - <dataset id="b54fb481e575bccc" hid="5" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>false</index> - </gff> - </options> - </track> - <track cat="Ignore Scale" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff"> - <metadata> - <dataset id="1ae74d26531588b0" hid="6" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>#ff00ff</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>false</index> - </gff> - </options> - </track> - <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff"> - <metadata> - <dataset id="1ae74d26531588b0" hid="6" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>score</method> - <algo>linear</algo> - <scales> - <type>automatic</type> - - </scales> - <scheme> - <type>opacity</type> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>false</index> - </gff> - </options> - </track> - <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff"> - <metadata> - <dataset id="1ae74d26531588b0" hid="6" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>score</method> - <algo>linear</algo> - <scales> - <type>automatic</type> - - </scales> - <scheme> - <type>opacity</type> - <color>#0000ff</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>false</index> - </gff> - </options> - </track> - <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff"> - <metadata> - <dataset id="1ae74d26531588b0" hid="6" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>score</method> - <algo>linear</algo> - <scales> - <type>manual</type> - - <min>0</min> - <max>1000</max> - </scales> - <scheme> - <type>opacity</type> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>false</index> - </gff> - </options> - </track> - <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff"> - <metadata> - <dataset id="1ae74d26531588b0" hid="6" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>score</method> - <algo>linear</algo> - <scales> - <type>manual</type> - - <min>0</min> - <max>1000</max> - </scales> - <scheme> - <type>opacity</type> - <color>#ff0000</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>false</index> - </gff> - </options> - </track> - <track cat="Realistic" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/0/3/0/dataset_030f551a-fd97-470e-ab58-328d8108783d.dat" ext="gff3" label="interpro.gff"> - <metadata> - <dataset id="440a6c2b5d9efe20" hid="7" - size="103.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="556" - comment_lines="2" - columns="9" - delimiter="__tc__" - attributes="11" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>false</index> - </gff> - </options> - </track> - <track cat="Realistic" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/a/b/b/dataset_abb36b76-2a3a-4353-919e-13c94629303f.dat" ext="gff3" label="2.gff"> - <metadata> - <dataset id="ea0b941dfbe636f8" hid="8" - size="326 bytes" - edam_format="format_1975" - file_ext="gff3" /> - <history id="8155e4b4bf1581ff" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="3" - comment_lines="3" - columns="9" - delimiter="__tc__" - attributes="4" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <match>cDNA_match</match> - <index>false</index> - </gff> - </options> - </track> - </tracks> - <plugins - ComboTrackSelector="" - Bookmarks="" - GCContent="" - BlastView="True" - theme="" - /> -</root>
--- a/test-data/menus/test.xml Thu Dec 31 16:00:42 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,175 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>11</gencode> - <genomes> - <genome path="/tmp/tmpqkd9zdgq/files/5/7/a/dataset_57af8674-e6c1-464b-9491-a7dade60d738.dat"> - <metadata> - <dataset id="61f03d5eef6f1538" hid="1" - size="171.6 KB" - edam_format="format_1929" - file_ext="fasta" /> - <history id="7b55dbb89df8f4e5" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </genome> - </genomes> - <general> - <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>true</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - <galaxyUrl>http://localhost</galaxyUrl> - </metadata> - <tracks> - <track cat="With menu or index" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/b/c/d/dataset_bcd9d5b3-9f0f-4350-8628-f282f26cb8d4.dat" ext="gff3" label="1.gff"> - <metadata> - <dataset id="d5b3e51b7b790121" hid="2" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="7b55dbb89df8f4e5" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - <menu> - <action>iframeDialog</action> - <label>Some menu item</label> - <title>Frame title</title> - <url>https://example.com/#!/?id={name}&q={type}&z="{end}"</url> - <iconClass>dijitIconNewTask</iconClass> - </menu> - <menu> - <action>newWindow</action> - <label>Another menu item</label> - <title>Frame title 2</title> - <url>https://example.com/#!/?id={name}&q={type}&z="{end}"</url> - <iconClass>dijitIconBookmark</iconClass> - </menu> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>false</index> - </gff> - </options> - </track> - <track cat="With menu or index" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/b/c/d/dataset_bcd9d5b3-9f0f-4350-8628-f282f26cb8d4.dat" ext="gff3" label="1.gff"> - <metadata> - <dataset id="d5b3e51b7b790121" hid="2" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="7b55dbb89df8f4e5" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <index>true</index> - </gff> - </options> - </track> - </tracks> - <plugins - ComboTrackSelector="" - Bookmarks="" - GCContent="" - BlastView="True" - theme="" - /> -</root>
--- a/test-data/track_config/test.xml Thu Dec 31 16:00:42 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,109 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>11</gencode> - <genomes> - <genome path="/tmp/tmpqkd9zdgq/files/d/0/a/dataset_d0a8a714-9666-4fe5-8083-976a4ba5c6bd.dat"> - <metadata> - <dataset id="c18708cec3343c17" 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="?" - data_lines="2881" - sequences="1" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </genome> - </genomes> - <general> - <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>true</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - <galaxyUrl>http://localhost</galaxyUrl> - </metadata> - <tracks> - <track cat="With canvas config" format="gene_calls" visibility="default_off"> - <files> - <trackFile path="/tmp/tmpqkd9zdgq/files/e/5/9/dataset_e597912a-188f-4152-afc7-fd537b2d5a0d.dat" ext="gff3" label="1.gff"> - <metadata> - <dataset id="5ca39fba41b940d1" hid="2" - size="2.3 KB" - edam_format="format_1975" - file_ext="gff3" /> - <history id="fa6d20d0fb68383f" - user_email="test@bx.psu.edu" - user_id="2" - display_name="test_history"/> - <metadata - dbkey="?" - data_lines="27" - comment_lines="19" - columns="9" - delimiter="__tc__" - attributes="6" - /> - <tool - tool_id="upload1" - tool_version="1.1.6" - /> - </metadata> - </trackFile> - </files> - - <options> - <style> - <overridePlugins>False</overridePlugins> - <overrideDraggable>False</overrideDraggable> - <className>feature</className> - <description>note,description</description> - <label>product,name,id</label> - <height>10px</height> - <maxHeight>600</maxHeight> - </style> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - <menus> - </menus> - <custom_config> - </custom_config> - - <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> - <transcriptType>transcript</transcriptType> - <subParts>exon</subParts> - <impliedUTRs>true</impliedUTRs> - <index>false</index> - </gff> - </options> - </track> - </tracks> - <plugins - ComboTrackSelector="" - Bookmarks="" - GCContent="" - BlastView="True" - theme="" - /> -</root>