Mercurial > repos > yating-l > jbrowsearchivecreator
changeset 47:1eb4adefd747 draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 97a743ee6d228c8a0a5778ec3cb6f68a2e22c8e3
| author | yating-l |
|---|---|
| date | Tue, 19 Jun 2018 17:39:12 -0400 |
| parents | 061da5d3a219 |
| children | 284c573f36a3 |
| files | TrackHub.py datatypes/Datatype.py jbrowseArchiveCreator.xml util/subtools.py |
| diffstat | 4 files changed, 17 insertions(+), 18 deletions(-) [+] |
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--- a/TrackHub.py Tue Jun 19 16:28:36 2018 -0400 +++ b/TrackHub.py Tue Jun 19 17:39:12 2018 -0400 @@ -56,7 +56,7 @@ def addTrack(self, trackDbObject): if trackDbObject['nameIndex'] == "true": - self.nameIndexTracksList.append(trackDbObject['trackLabel']) + self.nameIndexTrackList.append(trackDbObject['trackLabel']) if trackDbObject['dataType'].lower() == 'bam': subtools.add_track_json(self.trackList, trackDbObject['options']) elif trackDbObject['dataType'].lower() == 'bigwig': @@ -106,8 +106,9 @@ subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath) def _indexName(self): - subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList) - print "finished name index \n" + if self.nameIndexTrackList: + 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/datatypes/Datatype.py Tue Jun 19 16:28:36 2018 -0400 +++ b/datatypes/Datatype.py Tue Jun 19 17:39:12 2018 -0400 @@ -49,7 +49,6 @@ self.track = None self.trackSettings = dict() self.extraSettings = collections.OrderedDict() - self.nameIndex = False @staticmethod
--- a/jbrowseArchiveCreator.xml Tue Jun 19 16:28:36 2018 -0400 +++ b/jbrowseArchiveCreator.xml Tue Jun 19 17:39:12 2018 -0400 @@ -206,7 +206,7 @@ </valid> </sanitizer> </param> - <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> + <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"> @@ -224,7 +224,7 @@ type="data" label="Bed File" /> - <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> + <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_simple_repeats_option"> <param @@ -233,7 +233,7 @@ type="data" label="Bed Simple Repeats (Bed4+12) File" /> - <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> + <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_splice_junctions_option"> <param @@ -242,7 +242,7 @@ type="data" label="Bed Splice Junctions (Bed12+1) File" /> - <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> + <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_blast_alignment_option"> <param @@ -251,7 +251,7 @@ type="data" label="Bed Blast Alignments (Bed12+12) File" /> - <param name="nameIndex" type="boolean" value="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> + <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="bed_blat_alignment_option"> <param @@ -260,7 +260,7 @@ type="data" label="Bed BLAT Alignments (bigPsl) File" /> - <param name="nameIndex" type="boolean" value="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> + <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> </conditional> <param name="longLabel" type="text" size="30" label="Track label" /> @@ -287,7 +287,7 @@ </valid> </sanitizer> </param> - <param name="nameIndex" type="boolean" value="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> + <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 @@ -304,7 +304,7 @@ </valid> </sanitizer> </param> - <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> + <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 @@ -321,7 +321,7 @@ </valid> </sanitizer> </param> - <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> + <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 @@ -337,8 +337,8 @@ <add value="#"/> </valid> </sanitizer> - <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </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 Tue Jun 19 16:28:36 2018 -0400 +++ b/util/subtools.py Tue Jun 19 17:39:12 2018 -0400 @@ -383,10 +383,9 @@ return p def generate_names(outputFolder, nameIndexTrackList, hashBits=4): - array_call = ['generate-names.pl', '--hashBits', hashBits, '-v', '--completionLimit', '0', '--out', outputFolder] - if nameIndexTrackList: - array_call.append('--tracks') - array_call.append(','.join(nameIndexTrackList)) + array_call = ['generate-names.pl', '--hashBits', str(hashBits), '-v', '--completionLimit', '0', '--out', outputFolder] + array_call.append('--tracks') + array_call.append(','.join(nameIndexTrackList)) p = _handleExceptionAndCheckCall(array_call) return p