Mercurial > repos > yating-l > jbrowsearchivecreator
changeset 41:627cce51523f draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 2285eddcfe689d70d89571a045f204b74cc6890c-dirty
| author | yating-l |
|---|---|
| date | Sat, 28 Apr 2018 23:59:31 -0400 |
| parents | b1553f2a4942 |
| children | c5738ca0d815 |
| files | jbrowseArchiveCreator.xml tool_dependencies.xml tracks/CanvasFeatures.py |
| diffstat | 3 files changed, 9 insertions(+), 1 deletions(-) [+] |
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--- a/jbrowseArchiveCreator.xml Fri Apr 20 12:29:32 2018 -0400 +++ b/jbrowseArchiveCreator.xml Sat Apr 28 23:59:31 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.1"> +<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.2"> <description> This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin </description> @@ -7,6 +7,7 @@ </macros> <requirements> <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="2.6">tabix</requirement> <requirement type="package" version="1.9">numpy</requirement> <requirement type="package" version="1.68">biopython</requirement> <requirement type="package" version="340">ucsc_hac</requirement>
--- a/tool_dependencies.xml Fri Apr 20 12:29:32 2018 -0400 +++ b/tool_dependencies.xml Sat Apr 28 23:59:31 2018 -0400 @@ -4,6 +4,10 @@ <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> + <package name="tabix" version="2.6"> + <repository changeset_revision="54f8b9bf9b6c" name="package_tabix_0_2_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="ucsc_hac" version="340"> <repository changeset_revision="c6311d9e2443" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package>
--- a/tracks/CanvasFeatures.py Fri Apr 20 12:29:32 2018 -0400 +++ b/tracks/CanvasFeatures.py Sat Apr 28 23:59:31 2018 -0400 @@ -24,7 +24,10 @@ track['type'] = 'JBrowse/View/Track/' + self.trackType track['storeClass'] = 'JBrowse/Store/SeqFeature/GFF3Tabix' if self.dataType == 'gff': + # need .gff3.gz extension to index the name of the track with generate-name.pl track['urlTemplate'] = os.path.join('tracks', self.trackName + '.gff3.gz') + # needed to show match_part in Blat and Blast alignment as subfeatures + track['glyph'] = "JBrowse/View/FeatureGlyph/Segments" else: track['urlTemplate'] = os.path.join('tracks', self.trackName) track['label'] = self.trackLabel