Mercurial > repos > iuc > jbrowse
changeset 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 (2018-07-06) |
parents | 836d1aa3e89a |
children | 558d652cd681 |
files | jbrowse.xml macros.xml test-data/bam/154.bam test-data/bam/154.bam.bai test-data/bam/merlin-sample.bam test-data/bam/merlin-sample.bam.bai test-data/bam/test.xml |
diffstat | 7 files changed, 91 insertions(+), 26 deletions(-) [+] |
line wrap: on
line diff
--- a/jbrowse.xml Thu Nov 16 09:44:45 2017 -0500 +++ b/jbrowse.xml Fri Jul 06 06:10:18 2018 -0400 @@ -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[
--- a/macros.xml Thu Nov 16 09:44:45 2017 -0500 +++ b/macros.xml Fri Jul 06 06:10:18 2018 -0400 @@ -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:"/>
--- 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 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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