| Previous changeset 33:0ae74c70b267 (2019-08-30) Next changeset 35:3235aeb45c22 (2019-12-18) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" |
|
modified:
jbrowse.py jbrowse.xml macros.xml test-data/bam/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 |
|
added:
test-data/bed/test-3.bed test-data/bed/test-6.bed test-data/bed/test.xml |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 jbrowse.py --- a/jbrowse.py Fri Aug 30 03:36:39 2019 -0400 +++ b/jbrowse.py Wed Sep 11 09:40:36 2019 -0400 |
| [ |
| @@ -654,7 +654,8 @@ # Only index if not already done if not os.path.exists(dest): cmd = ['sort', '-k1,1', '-k2,2n', data] - self.subprocess_check_call(cmd, output=dest) + with open(dest, 'w') as handle: + self.subprocess_check_call(cmd, output=handle) self.subprocess_check_call(['bgzip', '-f', dest]) self.subprocess_check_call(['tabix', '-f', '-p', 'bed', dest + '.gz']) |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 jbrowse.xml --- a/jbrowse.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/jbrowse.xml Wed Sep 11 09:40:36 2019 -0400 |
| b |
| @@ -673,6 +673,23 @@ <param name="gencode" value="11" /> <param name="standalone" value="Data Directory" /> <repeat name="track_groups"> + <param name="category" value="Default" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gene_calls"/> + <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/> + </conditional> + </repeat> + </repeat> + <param name="uglyTestingHack" value="enabled" /> + <output name="output" file="bed/test.xml" lines_diff="32"/> + </test> + <test> + <param name="reference_genome|genome_type_select" value="history"/> + <param name="reference_genome|genome" value="merlin.fa"/> + <param name="gencode" value="11" /> + <param name="standalone" value="Data Directory" /> + <repeat name="track_groups"> <param name="category" value="Auto Coloured" /> <repeat name="data_tracks"> <conditional name="data_format"> @@ -861,7 +878,7 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gff3/test.xml" lines_diff="170" /> + <output name="output" file="gff3/test.xml" lines_diff="240" /> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 macros.xml --- a/macros.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/macros.xml Wed Sep 11 09:40:36 2019 -0400 |
| [ |
| @@ -14,7 +14,7 @@ </requirements> </xml> <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> - <token name="@WRAPPER_VERSION@">galaxy4</token> + <token name="@WRAPPER_VERSION@">galaxy5</token> <token name="@ATTRIBUTION@"><![CDATA[ **Attribution** |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/bam/test.xml --- a/test-data/bam/test.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/test-data/bam/test.xml Wed Sep 11 09:40:36 2019 -0400 |
| [ |
| b'@@ -3,13 +3,13 @@\n <metadata>\n <gencode>11</gencode>\n <genomes>\n- <genome path="/tmp/tmpWtvfKr/files/000/dataset_20.dat">\n+ <genome path="/tmp/tmpqkd9zdgq/files/d/3/d/dataset_d3d20b83-6a77-4e76-bb7e-3b9fe7261453.dat">\n <metadata>\n- <dataset id="b28067233c6d9fa0" hid="1"\n+ <dataset id="238993350abc9bfd" hid="1"\n size="171.6 KB"\n edam_format="format_1929"\n file_ext="fasta" />\n- <history id="fa6d20d0fb68383f"\n+ <history id="a90a30fafe298e1e"\n user_email="test@bx.psu.edu"\n user_id="2"\n display_name="test_history"/>\n@@ -42,13 +42,13 @@\n <tracks>\n <track cat="Auto Coloured" format="pileup" visibility="default_off">\n <files>\n- <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_21.dat" ext="bam" label="merlin-sample.bam">\n+ <trackFile path="/tmp/tmpqkd9zdgq/files/6/a/0/dataset_6a00d93a-ee34-42d5-897b-9470d6c71e1f.dat" ext="bam" label="merlin-sample.bam">\n <metadata>\n- <dataset id="c18708cec3343c17" hid="2"\n+ <dataset id="adba32ec9811aba7" hid="2"\n size="12.9 KB"\n edam_format="format_2572"\n file_ext="bam" />\n- <history id="fa6d20d0fb68383f"\n+ <history id="a90a30fafe298e1e"\n user_email="test@bx.psu.edu"\n user_id="2"\n display_name="test_history"/>\n@@ -56,12 +56,10 @@\n dbkey="?"\n bam_version="1.3"\n sort_order="coordinate"\n- 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__]"\n+ 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__]"\n reference_lengths="[172788]"\n- 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__'..b'__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 7f6200e95730 on: __sq__CIGAR__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 7f6200e95d60 on: __sq__MRNM__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 7f6200e95d08 on: __sq__MPOS__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 7f6200e95c58 on: __sq__ISIZE__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 7f6200e952b8 on: __sq__SEQ__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 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__]"\n- bam_index="__lt__galaxy.model.MetadataFile object at 0x7f6200f6d1d0__gt__"\n+ bam_index="__lt__galaxy.model.MetadataFile(1) at 0x7f3de95da7d0__gt__"\n />\n <tool\n tool_id="upload1"\n@@ -78,7 +76,7 @@\n <pileup>\n <auto_snp>false</auto_snp>\n <bam_indices>\n- <bam_index>/tmp/tmpWtvfKr/files/_metadata_files/000/metadata_1.dat</bam_index>\n+ <bam_index>/tmp/tmpqkd9zdgq/files/_metadata_files/a/5/2/metadata_a520581b-e8cc-43e5-8514-3379cd5eaafb.dat</bam_index>\n </bam_indices>\n <chunkSizeLimit>5000000</chunkSizeLimit>\n </pileup>\n' |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/bed/test-3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed/test-3.bed Wed Sep 11 09:40:36 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Merlin 49 1452 +Merlin 1457 2557 +Merlin 2557 3630 |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/bed/test-6.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed/test-6.bed Wed Sep 11 09:40:36 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Merlin 49 1452 chromosomal_replication_initiator_protein_DnaA 0 + +Merlin 1457 2557 DNA_polymerase_III_subunit_beta 0 + +Merlin 2557 3630 DNA_replication_and_repair_protein_RecF 0 + |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/bed/test.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed/test.xml Wed Sep 11 09:40:36 2019 -0400 |
| [ |
| @@ -0,0 +1,136 @@ +<?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> |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/custom_config/test.xml --- a/test-data/custom_config/test.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/test-data/custom_config/test.xml Wed Sep 11 09:40:36 2019 -0400 |
| b |
| @@ -3,13 +3,13 @@ <metadata> <gencode>11</gencode> <genomes> - <genome path="/tmp/tmpWtvfKr/files/000/dataset_17.dat"> + <genome path="/tmp/tmpqkd9zdgq/files/1/a/7/dataset_1a77d084-9f64-48b9-802b-787e0e86c7b1.dat"> <metadata> - <dataset id="27ee89e2e3d631e0" hid="1" + <dataset id="a1e670e1ea0da54b" hid="1" size="171.6 KB" edam_format="format_1929" file_ext="fasta" /> - <history id="7b55dbb89df8f4e5" + <history id="683bc220e21425bb" user_email="test@bx.psu.edu" user_id="2" display_name="test_history"/> @@ -42,13 +42,13 @@ <tracks> <track cat="With custom track config" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_18.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpqkd9zdgq/files/a/4/a/dataset_a4a9adc4-f3d3-4c05-8074-69e01ace1c78.dat" ext="gff3" label="1.gff"> <metadata> - <dataset id="61f03d5eef6f1538" hid="2" + <dataset id="9a22496ee796fbfc" hid="2" size="2.3 KB" edam_format="format_1975" file_ext="gff3" /> - <history id="7b55dbb89df8f4e5" + <history id="683bc220e21425bb" user_email="test@bx.psu.edu" user_id="2" display_name="test_history"/> @@ -72,7 +72,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature2</className> + <className>feature</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -103,7 +103,6 @@ <gff> <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <topLevelFeatures>mRNA</topLevelFeatures> <index>false</index> </gff> </options> |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/endpoints/test.xml --- a/test-data/endpoints/test.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/test-data/endpoints/test.xml Wed Sep 11 09:40:36 2019 -0400 |
| b |
| @@ -3,13 +3,13 @@ <metadata> <gencode>11</gencode> <genomes> - <genome path="/tmp/tmpdcb31B/files/000/dataset_24.dat"> + <genome path="/tmp/tmpqkd9zdgq/files/9/5/5/dataset_955a2615-e4c3-4ccc-ae7b-749a589abc12.dat"> <metadata> - <dataset id="a1e670e1ea0da54b" hid="1" + <dataset id="27a22803849b1486" hid="1" size="171.6 KB" edam_format="format_1929" file_ext="fasta" /> - <history id="a90a30fafe298e1e" + <history id="5449172d6ff5669b" user_email="test@bx.psu.edu" user_id="2" display_name="test_history"/> |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/gencode/test-1.xml --- a/test-data/gencode/test-1.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/test-data/gencode/test-1.xml Wed Sep 11 09:40:36 2019 -0400 |
| b |
| @@ -3,7 +3,7 @@ <metadata> <gencode>1</gencode> <genomes> - <genome path="/tmp/tmpZA6JJa/files/000/dataset_1.dat"> + <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" |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/gencode/test-data_table.xml --- a/test-data/gencode/test-data_table.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/test-data/gencode/test-data_table.xml Wed Sep 11 09:40:36 2019 -0400 |
| b |
| @@ -3,7 +3,7 @@ <metadata> <gencode>1</gencode> <genomes> - <genome path="/home/abretaud/iuc_tools_abretaud/tools/jbrowse/test-data/merlin.fa"> + <genome path="/home/hxr/arbeit/tools-iuc/tools/jbrowse/test-data/merlin.fa"> <metadata /> </genome>s </genomes> @@ -19,7 +19,7 @@ <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> - <galaxyUrl>http://localhost:8080</galaxyUrl> + <galaxyUrl>http://localhost</galaxyUrl> </metadata> <tracks> </tracks> |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/gencode/test.xml --- a/test-data/gencode/test.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/test-data/gencode/test.xml Wed Sep 11 09:40:36 2019 -0400 |
| b |
| @@ -3,7 +3,7 @@ <metadata> <gencode>11</gencode> <genomes> - <genome path="/tmp/tmpZA6JJa/files/000/dataset_3.dat"> + <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" |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/gff3/test.xml --- a/test-data/gff3/test.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/test-data/gff3/test.xml Wed Sep 11 09:40:36 2019 -0400 |
| b |
| b'@@ -3,13 +3,13 @@\n <metadata>\n <gencode>11</gencode>\n <genomes>\n- <genome path="/tmp/tmpTx5wXw/files/000/dataset_5.dat">\n+ <genome path="/tmp/tmpqkd9zdgq/files/b/f/a/dataset_bfad32fe-cc05-405c-965c-6fe9b7a36908.dat">\n <metadata>\n- <dataset id="7b55dbb89df8f4e5" hid="1"\n+ <dataset id="b842d972534ccb3e" hid="1"\n size="171.6 KB"\n edam_format="format_1929"\n file_ext="fasta" />\n- <history id="54f2a3a23292eb07"\n+ <history id="8155e4b4bf1581ff"\n user_email="test@bx.psu.edu"\n user_id="2"\n display_name="test_history"/>\n@@ -42,13 +42,13 @@\n <tracks>\n <track cat="Auto Coloured" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_6.dat" ext="gff3" label="gff3/A.gff">\n+ <trackFile path="/tmp/tmpqkd9zdgq/files/7/6/2/dataset_7625da24-6a53-41c2-a7fc-c5c9719deccc.dat" ext="gff3" label="A.gff">\n <metadata>\n- <dataset id="fa6d20d0fb68383f" hid="2"\n+ <dataset id="5449172d6ff5669b" hid="2"\n size="2.3 KB"\n edam_format="format_1975"\n file_ext="gff3" />\n- <history id="54f2a3a23292eb07"\n+ <history id="8155e4b4bf1581ff"\n user_email="test@bx.psu.edu"\n user_id="2"\n display_name="test_history"/>\n@@ -66,13 +66,13 @@\n />\n </metadata>\n </trackFile>\n- <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_7.dat" ext="gff3" label="gff3/B.gff">\n+ <trackFile path="/tmp/tmpqkd9zdgq/files/c/f/c/dataset_cfcde690-dc99-4152-87ef-0936eb90f2ca.dat" ext="gff3" label="B.gff">\n <metadata>\n- <dataset id="683bc220e21425bb" hid="3"\n+ <dataset id="9ce08b2254e4d5ed" hid="3"\n size="2.3 KB"\n edam_format="format_1975"\n file_ext="gff3" />\n- <history id="54f2a3a23292eb07"\n+ <history id="8155e4b4bf1581ff"\n user_email="test@bx.psu.edu"\n user_id="2"\n display_name="test_history"/>\n@@ -90,13 +90,13 @@\n />\n </metadata>\n </trackFile>\n- <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_8.dat" ext="gff3" label="gff3/C.gff">\n+ <trackFile path="/tmp/tmpqkd9zdgq/files/1/c/4/dataset_1c41cecd-9fc6-47b5-9f0b-b7bb73498675.dat" ext="gff3" label="C.gff">\n <metadata>\n- <dataset id="a90a30fafe298e1e" hid="4"\n+ <dataset id="80b8022ff3f677b7" hid="4"\n size="2.3 KB"\n edam_format="format_1975"\n file_ext="gff3" />\n- <history id="54f2a3a23292eb07"\n+ <history id="8155e4b4bf1581ff"\n user_email="test@bx.psu.edu"\n user_id="2"\n display_name="test_history"/>\n@@ -114,13 +114,13 @@\n />\n </metadata>\n </trackFile>\n- <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_9.dat" ext="gff3" label="gff3/D.gff">\n+ <trackFile path="/tmp/tmpqkd9zdgq/files/5/b/3/dataset_5b33c8ff-b12b-4307-a35c-92ea8571dc04.dat" ext="gff3" label="D.gff">\n <metadata>\n- <dataset id="b842d972534ccb3e" hid="5"\n+ <dataset id="b54fb481e575bccc" hid="5"\n size="2.3 KB"\n edam_format="format_1975"\n file_ext="gff3" />\n- '..b'2a3a23292eb07"\n+ <history id="8155e4b4bf1581ff"\n user_email="test@bx.psu.edu"\n user_id="2"\n display_name="test_history"/>\n@@ -407,20 +403,19 @@\n \n <gff>\n <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>\n- <topLevelFeatures>mRNA</topLevelFeatures>\n <index>false</index>\n </gff>\n </options>\n </track>\n <track cat="Scaled Colour" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff">\n+ <trackFile path="/tmp/tmpqkd9zdgq/files/2/d/4/dataset_2d49732b-93ef-4018-971f-5a3b92e9ecd0.dat" ext="gff3" label="1.gff">\n <metadata>\n- <dataset id="5449172d6ff5669b" hid="6"\n+ <dataset id="1ae74d26531588b0" hid="6"\n size="2.3 KB"\n edam_format="format_1975"\n file_ext="gff3" />\n- <history id="54f2a3a23292eb07"\n+ <history id="8155e4b4bf1581ff"\n user_email="test@bx.psu.edu"\n user_id="2"\n display_name="test_history"/>\n@@ -471,20 +466,19 @@\n \n <gff>\n <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>\n- <topLevelFeatures>mRNA</topLevelFeatures>\n <index>false</index>\n </gff>\n </options>\n </track>\n <track cat="Realistic" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_11.dat" ext="gff3" label="gff3/interpro.gff">\n+ <trackFile path="/tmp/tmpqkd9zdgq/files/0/3/0/dataset_030f551a-fd97-470e-ab58-328d8108783d.dat" ext="gff3" label="interpro.gff">\n <metadata>\n- <dataset id="9ce08b2254e4d5ed" hid="7"\n+ <dataset id="440a6c2b5d9efe20" hid="7"\n size="103.3 KB"\n edam_format="format_1975"\n file_ext="gff3" />\n- <history id="54f2a3a23292eb07"\n+ <history id="8155e4b4bf1581ff"\n user_email="test@bx.psu.edu"\n user_id="2"\n display_name="test_history"/>\n@@ -527,20 +521,19 @@\n \n <gff>\n <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>\n- <topLevelFeatures>mRNA</topLevelFeatures>\n <index>false</index>\n </gff>\n </options>\n </track>\n <track cat="Realistic" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_12.dat" ext="gff3" label="gff3/2.gff">\n+ <trackFile path="/tmp/tmpqkd9zdgq/files/a/b/b/dataset_abb36b76-2a3a-4353-919e-13c94629303f.dat" ext="gff3" label="2.gff">\n <metadata>\n- <dataset id="80b8022ff3f677b7" hid="8"\n+ <dataset id="ea0b941dfbe636f8" hid="8"\n size="326 bytes"\n edam_format="format_1975"\n file_ext="gff3" />\n- <history id="54f2a3a23292eb07"\n+ <history id="8155e4b4bf1581ff"\n user_email="test@bx.psu.edu"\n user_id="2"\n display_name="test_history"/>\n@@ -583,7 +576,6 @@\n \n <gff>\n <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>\n- <topLevelFeatures>mRNA</topLevelFeatures>\n <match>cDNA_match</match>\n <index>false</index>\n </gff>\n' |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/menus/test.xml --- a/test-data/menus/test.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/test-data/menus/test.xml Wed Sep 11 09:40:36 2019 -0400 |
| b |
| @@ -3,13 +3,13 @@ <metadata> <gencode>11</gencode> <genomes> - <genome path="/tmp/tmpWtvfKr/files/000/dataset_14.dat"> + <genome path="/tmp/tmpqkd9zdgq/files/5/7/a/dataset_57af8674-e6c1-464b-9491-a7dade60d738.dat"> <metadata> - <dataset id="1ae74d26531588b0" hid="1" + <dataset id="61f03d5eef6f1538" hid="1" size="171.6 KB" edam_format="format_1929" file_ext="fasta" /> - <history id="8155e4b4bf1581ff" + <history id="7b55dbb89df8f4e5" user_email="test@bx.psu.edu" user_id="2" display_name="test_history"/> @@ -42,13 +42,13 @@ <tracks> <track cat="With menu or index" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_15.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpqkd9zdgq/files/b/c/d/dataset_bcd9d5b3-9f0f-4350-8628-f282f26cb8d4.dat" ext="gff3" label="1.gff"> <metadata> - <dataset id="440a6c2b5d9efe20" hid="2" + <dataset id="d5b3e51b7b790121" hid="2" size="2.3 KB" edam_format="format_1975" file_ext="gff3" /> - <history id="8155e4b4bf1581ff" + <history id="7b55dbb89df8f4e5" user_email="test@bx.psu.edu" user_id="2" display_name="test_history"/> @@ -72,7 +72,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature2</className> + <className>feature</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -105,20 +105,19 @@ <gff> <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <topLevelFeatures>mRNA</topLevelFeatures> <index>false</index> </gff> </options> </track> <track cat="With menu or index" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_15.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpqkd9zdgq/files/b/c/d/dataset_bcd9d5b3-9f0f-4350-8628-f282f26cb8d4.dat" ext="gff3" label="1.gff"> <metadata> - <dataset id="440a6c2b5d9efe20" hid="2" + <dataset id="d5b3e51b7b790121" hid="2" size="2.3 KB" edam_format="format_1975" file_ext="gff3" /> - <history id="8155e4b4bf1581ff" + <history id="7b55dbb89df8f4e5" user_email="test@bx.psu.edu" user_id="2" display_name="test_history"/> @@ -142,7 +141,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature2</className> + <className>feature</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -161,7 +160,6 @@ <gff> <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> - <topLevelFeatures>mRNA</topLevelFeatures> <index>true</index> </gff> </options> |
| b |
| diff -r 0ae74c70b267 -r 9de82b4963e6 test-data/track_config/test.xml --- a/test-data/track_config/test.xml Fri Aug 30 03:36:39 2019 -0400 +++ b/test-data/track_config/test.xml Wed Sep 11 09:40:36 2019 -0400 |
| b |
| @@ -3,13 +3,13 @@ <metadata> <gencode>11</gencode> <genomes> - <genome path="/tmp/tmpWtvfKr/files/000/dataset_17.dat"> + <genome path="/tmp/tmpqkd9zdgq/files/d/0/a/dataset_d0a8a714-9666-4fe5-8083-976a4ba5c6bd.dat"> <metadata> - <dataset id="27ee89e2e3d631e0" hid="1" + <dataset id="c18708cec3343c17" hid="1" size="171.6 KB" edam_format="format_1929" file_ext="fasta" /> - <history id="7b55dbb89df8f4e5" + <history id="fa6d20d0fb68383f" user_email="test@bx.psu.edu" user_id="2" display_name="test_history"/> @@ -42,13 +42,13 @@ <tracks> <track cat="With canvas config" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_18.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpqkd9zdgq/files/e/5/9/dataset_e597912a-188f-4152-afc7-fd537b2d5a0d.dat" ext="gff3" label="1.gff"> <metadata> - <dataset id="61f03d5eef6f1538" hid="2" + <dataset id="5ca39fba41b940d1" hid="2" size="2.3 KB" edam_format="format_1975" file_ext="gff3" /> - <history id="7b55dbb89df8f4e5" + <history id="fa6d20d0fb68383f" user_email="test@bx.psu.edu" user_id="2" display_name="test_history"/> @@ -72,7 +72,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature2</className> + <className>feature</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> |