Mercurial > repos > yating-l > jbrowsearchivecreator
changeset 50:804e7217f27c draft default tip
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3afab1eb0da4823419945c523a1d37cd5973e7f6-dirty
| author | yating-l |
|---|---|
| date | Fri, 20 Jul 2018 11:38:01 -0400 |
| parents | be34d213ec6a |
| children | |
| files | TrackHub.py jbrowseArchiveCreator.xml util/subtools.py |
| diffstat | 3 files changed, 11 insertions(+), 11 deletions(-) [+] |
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--- a/TrackHub.py Wed Jun 20 17:23:48 2018 -0400 +++ b/TrackHub.py Fri Jul 20 11:38:01 2018 -0400 @@ -106,9 +106,8 @@ subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath) def _indexName(self): - if self.nameIndexTrackList: - subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList) - print "finished name index \n" + subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList) + print "finished name index \n" def _outHtml(self): mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
--- a/jbrowseArchiveCreator.xml Wed Jun 20 17:23:48 2018 -0400 +++ b/jbrowseArchiveCreator.xml Fri Jul 20 11:38:01 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.0"> +<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.2"> <description> This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin </description> @@ -199,6 +199,7 @@ type="data" label="BAM File" /> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> <param name="longLabel" type="text" size="30" value = "Sequence Alignment" label="Track label" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> @@ -207,7 +208,6 @@ </valid> </sanitizer> </param> - <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="bed"> <conditional name="bedChoice"> @@ -296,6 +296,7 @@ <option value="FlyBase">FlyBase</option> <option value="Others">Others</option> </param> + <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> @@ -304,7 +305,6 @@ </valid> </sanitizer> </param> - <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="bigwig"> <param @@ -313,6 +313,7 @@ type="data" label="BIGWIG File" /> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> <param name="longLabel" type="text" size="30" value="Sequence Coverage" label="Track label" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> @@ -321,7 +322,6 @@ </valid> </sanitizer> </param> - <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="gff3"> <param @@ -330,6 +330,7 @@ type="data" label="GFF3 File" /> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> @@ -338,7 +339,6 @@ </valid> </sanitizer> </param> - <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="gtf"> <param @@ -347,6 +347,7 @@ type="data" label="GTF File" /> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> <param name="longLabel" type="text" size="30" value="Assembled Transcripts" label="Track name" /> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> @@ -355,7 +356,6 @@ </valid> </sanitizer> </param> - <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> </conditional> </repeat>
--- a/util/subtools.py Wed Jun 20 17:23:48 2018 -0400 +++ b/util/subtools.py Fri Jul 20 11:38:01 2018 -0400 @@ -384,8 +384,9 @@ def generate_names(outputFolder, nameIndexTrackList, hashBits=4): array_call = ['generate-names.pl', '--hashBits', str(hashBits), '-v', '--completionLimit', '0', '--out', outputFolder] - array_call.append('--tracks') - array_call.append(','.join(nameIndexTrackList)) + if nameIndexTrackList: + array_call.append('--tracks') + array_call.append(','.join(nameIndexTrackList)) p = _handleExceptionAndCheckCall(array_call) return p