| Previous changeset 18:836d1aa3e89a (2017-11-16) Next changeset 20:558d652cd681 (2018-08-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47 |
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modified:
jbrowse.xml macros.xml test-data/bam/test.xml |
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added:
test-data/bam/merlin-sample.bam test-data/bam/merlin-sample.bam.bai |
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removed:
test-data/bam/154.bam test-data/bam/154.bam.bai |
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| diff -r 836d1aa3e89a -r 8f33c9fbc119 jbrowse.xml --- a/jbrowse.xml Thu Nov 16 09:44:45 2017 -0500 +++ b/jbrowse.xml Fri Jul 06 06:10:18 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3"> +<tool id="jbrowse" name="JBrowse" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> <description>genome browser</description> <macros> <import>macros.xml</import> @@ -601,7 +601,7 @@ <param name="gencode" value="1" /> <param name="standalone" value="Data Directory" /> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gencode/test-1.xml" lines_diff="4" /> + <output name="output" file="gencode/test-1.xml" lines_diff="14"/> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -805,7 +805,7 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gff3/test.xml" lines_diff="64" /> + <output name="output" file="gff3/test.xml" lines_diff="256" /> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -908,13 +908,33 @@ <output name="output" file="track_config/test.xml" lines_diff="26"/> </test> <test> + <param name="reference_genome|genome_type_select" value="history"/> + <param name="reference_genome|genomes" 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"> + <param name="data_format_select" value="pileup"/> + <param name="annotation" value="bam/merlin-sample.bam"/> + </conditional> + </repeat> + </repeat> + + <param name="uglyTestingHack" value="enabled" /> + <output name="output" file="bam/test.xml" lines_diff="48"/> + </test> + + <test> <!-- data_table --> <param name="reference_genome|genome_type_select" value="indexed"/> <param name="reference_genome|genomes" value="merlin"/> <param name="gencode" value="1" /> <param name="standalone" value="Data Directory" /> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gencode/test-data_table.xml" lines_diff="4" /> + <output name="output" file="gencode/test-data_table.xml" lines_diff="6" /> </test> </tests> <help><![CDATA[ |
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| diff -r 836d1aa3e89a -r 8f33c9fbc119 macros.xml --- a/macros.xml Thu Nov 16 09:44:45 2017 -0500 +++ b/macros.xml Fri Jul 06 06:10:18 2018 -0400 |
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| @@ -1,8 +1,9 @@ <?xml version="1.0"?> <macros> + <token name="@TOOL_VERSION@">1.12.5</token> <xml name="requirements"> <requirements> - <requirement type="package" version="1.12.3">jbrowse</requirement> + <requirement type="package" version="@TOOL_VERSION@">jbrowse</requirement> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.66">biopython</requirement> <requirement type="package" version="0.6.2">bcbiogff</requirement> @@ -12,7 +13,7 @@ </requirements> </xml> <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> - <token name="@WRAPPER_VERSION@">0.7.0</token> + <token name="@WRAPPER_VERSION@">galaxy0</token> <xml name="stdio"> <stdio> <exit_code range="1:"/> |
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| diff -r 836d1aa3e89a -r 8f33c9fbc119 test-data/bam/154.bam |
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| Binary file test-data/bam/154.bam has changed |
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| diff -r 836d1aa3e89a -r 8f33c9fbc119 test-data/bam/154.bam.bai |
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| Binary file test-data/bam/154.bam.bai has changed |
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| diff -r 836d1aa3e89a -r 8f33c9fbc119 test-data/bam/merlin-sample.bam |
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| Binary file test-data/bam/merlin-sample.bam has changed |
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| diff -r 836d1aa3e89a -r 8f33c9fbc119 test-data/bam/merlin-sample.bam.bai |
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| Binary file test-data/bam/merlin-sample.bam.bai has changed |
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| diff -r 836d1aa3e89a -r 8f33c9fbc119 test-data/bam/test.xml --- 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 |
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| b'@@ -3,46 +3,90 @@\n <metadata>\n <gencode>11</gencode>\n <genomes>\n- <genome>test-data/merlin.fa</genome>\n+ <genome path="/tmp/tmpfqQZDj/files/000/dataset_2.dat">\n+ <metadata>\n+ <dataset id="9a22496ee796fbfc" hid="1"\n+ size="171.6 KB"\n+ edam_format="format_1929"\n+ file_ext="fasta" />\n+ <history id="fa6d20d0fb68383f"\n+ user_email="test@bx.psu.edu"\n+ user_id="2"\n+ display_name="test_history"/>\n+ <metadata\n+ dbkey="hg17"\n+ data_lines="2881"\n+ sequences="1"\n+ />\n+ <tool\n+ tool_id="upload1"\n+ tool_version="1.1.4"\n+ />\n+ </metadata>\n+ </genome>\n </genomes>\n <general>\n <defaultLocation></defaultLocation>\n- <trackPadding>40</trackPadding>\n+ <trackPadding>20</trackPadding>\n+\n <shareLink>true</shareLink>\n <aboutDescription></aboutDescription>\n <show_tracklist>true</show_tracklist>\n <show_nav>true</show_nav>\n- <show_overview>false</show_overview>\n+ <show_overview>true</show_overview>\n <show_menu>true</show_menu>\n <hideGenomeOptions>false</hideGenomeOptions>\n </general>\n+ <galaxyUrl>http://localhost</galaxyUrl>\n </metadata>\n <tracks>\n- <track cat="Default" format="pileup">\n+ <track cat="Aligned reads" format="pileup" visibility="default_off">\n <files>\n- <trackFile path="test-data/bam/154.bam" ext="bam" label="Basic"/>\n+ <trackFile path="/tmp/tmpfqQZDj/files/000/dataset_1.dat" ext="bam" label="merlin-sample.bam">\n+ <metadata>\n+ <dataset id="2891970512fa2d5a" hid="1"\n+ size="12.9 KB"\n+ edam_format="format_2572"\n+ file_ext="bam" />\n+ <history id="2891970512fa2d5a"\n+ user_email="planemo@galaxyproject.org"\n+ user_id="1"\n+ display_name="Unnamed history"/>\n+ <metadata\n+ dbkey="hg17"\n+ bam_index="__lt__galaxy.model.MetadataFile object at 0x7fc42c1d18d0__gt__"\n+ bam_version="1.3"\n+ sort_order="coordinate"\n+ read_groups=""\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 7fc4484b3170 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 7fc44857fb90 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___'..b'_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 7fc448256260 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 7fc4482560a8 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 7fc448256470 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 7fc448256628 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 7fc448256158 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 7fc448256730 on: __sq__OPT__sq__]"\n+ />\n+ <tool\n+ tool_id="upload1"\n+ tool_version="1.1.4"\n+ />\n+ </metadata>\n+ </trackFile>\n </files>\n+\n <options>\n+\n <pileup>\n <auto_snp>false</auto_snp>\n <bam_indices>\n- <bam_index>test-data/bam/154.bam.bai</bam_index>\n- </bam_indices>\n- </pileup>\n- </options>\n- </track>\n- <track cat="Default" format="pileup">\n- <files>\n- <trackFile path="test-data/bam/154.bam" ext="bam" label="Auto-SNP"/>\n- </files>\n- <options>\n- <pileup>\n- <auto_snp>true</auto_snp>\n- <bam_indices>\n- <bam_index>test-data/bam/154.bam.bai</bam_index>\n+ <bam_index>/tmp/tmpfqQZDj/files/_metadata_files/000/metadata_1.dat</bam_index>\n </bam_indices>\n </pileup>\n </options>\n </track>\n </tracks>\n-</root>\n+ <plugins\n+ ComboTrackSelector=""\n+ Bookmarks=""\n+ GCContent=""\n+ theme=""\n+ />\n+</root>\n\\ No newline at end of file\n' |