Mercurial > repos > iuc > jbrowse
changeset 18:836d1aa3e89a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
| author | iuc |
|---|---|
| date | Thu, 16 Nov 2017 09:44:45 -0500 |
| parents | ff11d442feed |
| children | 8f33c9fbc119 |
| files | jbrowse.xml readme.rst test-data/all_fasta.loc test-data/gencode/test-data_table.xml tool_data_table_conf.xml.test |
| diffstat | 5 files changed, 79 insertions(+), 7 deletions(-) [+] |
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--- a/jbrowse.xml Wed Nov 15 15:15:27 2017 -0500 +++ b/jbrowse.xml Thu Nov 16 09:44:45 2017 -0500 @@ -1,11 +1,11 @@ -<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.2"> +<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3"> <description>genome browser</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> - <version_command>python jbrowse.py --version</version_command> + <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command> <command><![CDATA[ #if $action.action_select == "create": @@ -19,7 +19,7 @@ cp $trackxml $output.files_path/galaxy.xml && ## Once that's done, we run the python script to handle the real work -python $__tool_directory__/jbrowse.py +python '$__tool_directory__/jbrowse.py' --jbrowse \${JBROWSE_SOURCE_DIR} #if str($standalone) == "Complete": @@ -73,7 +73,9 @@ <gencode>$gencode</gencode> <genomes> #if str($reference_genome.genome_type_select) == "indexed": - <genome>${reference_genome.genomes.fields.path}</genome> + <genome path="${reference_genome.genomes.fields.path}"> + <metadata /> + </genome>s #else #for $genome in $reference_genome.genomes: <genome path="$genome"> @@ -495,7 +497,8 @@ help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')" optional="True"/> </section> - </when> + </when> + <when value="BlastView/View/Track/CanvasFeatures" /> </conditional> <expand macro="track_styling" /> <expand macro="color_selection" /> @@ -904,6 +907,15 @@ <param name="uglyTestingHack" value="enabled" /> <output name="output" file="track_config/test.xml" lines_diff="26"/> </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" /> + </test> </tests> <help><![CDATA[ JBrowse-in-Galaxy
--- a/readme.rst Wed Nov 15 15:15:27 2017 -0500 +++ b/readme.rst Thu Nov 16 09:44:45 2017 -0500 @@ -7,7 +7,7 @@ Thus, it makes an ideal fit with Galaxy, especially for use as a workflow summary. E.g. annotate a genome, then visualise all of the associated datasets as an interactive HTML page. This tool MUST be whitelisted -(or ``sanitize_all_html=False``) to function correctly. +(or ``sanitize_all_html=False`` in galaxy.ini) to function correctly. Installation ============ @@ -17,7 +17,7 @@ Running Locally =============== -The Galaxy tool interface writes out a yaml file which is then used to generate +The Galaxy tool interface writes out a xml file which is then used to generate the visualizations. An example used during development/testing can be seen in `test-data/*/test.xml`. The format is in no way rigorously defined and is likely to change at any time! Beware. ;) @@ -25,6 +25,8 @@ History ======= +- 0.7 Support for plugins (currently GC Content, Bookmarks, ComboTrackSelector), + track metadata - 0.5.2 Support for CanvasFeatures options. - 0.5.1 Support for contextual menus. Conda tests. - 0.5 Update existing instances on disk. Index names. Support HTML tracks
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Thu Nov 16 09:44:45 2017 -0500 @@ -0,0 +1,19 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# +merlin merlin Merlin ${__HERE__}/merlin.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gencode/test-data_table.xml Thu Nov 16 09:44:45 2017 -0500 @@ -0,0 +1,32 @@ +<?xml version="1.0"?> +<root> + <metadata> + <gencode>1</gencode> + <genomes> + <genome path="/home/abretaud/iuc_tools_abretaud/tools/jbrowse/test-data/merlin.fa"> + <metadata /> + </genome>s + </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>20</trackPadding> + + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>true</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> + <galaxyUrl>http://localhost:8080</galaxyUrl> + </metadata> + <tracks> + </tracks> + <plugins + ComboTrackSelector="" + Bookmarks="" + GCContent="" + theme="" + /> +</root>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Nov 16 09:44:45 2017 -0500 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables>