Mercurial > repos > yating-l > hubarchivecreator
changeset 62:4c4e8941feda draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5bbecd016ad3a784ad030cb82a09a3ac40dc6060-dirty
| author | yating-l |
|---|---|
| date | Mon, 10 Jul 2017 17:06:11 -0400 |
| parents | 68aeb6482069 |
| children | e50fc56bd10d |
| files | Bed.py cytoBand.py hubArchiveCreator.xml templates/trackDb/layout.txt |
| diffstat | 4 files changed, 19 insertions(+), 4 deletions(-) [+] |
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--- a/Bed.py Mon Jul 03 17:24:49 2017 -0400 +++ b/Bed.py Mon Jul 10 17:06:11 2017 -0400 @@ -44,6 +44,8 @@ subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name, + typeOption='bed4', + tab='True', extraIndex='name' )
--- a/cytoBand.py Mon Jul 03 17:24:49 2017 -0400 +++ b/cytoBand.py Mon Jul 10 17:06:11 2017 -0400 @@ -41,7 +41,8 @@ subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name, - typeOption='bed4', + typeOption='bed4+1', + tab='True', autoSql=auto_sql_option) # Create the Track Object
--- a/hubArchiveCreator.xml Mon Jul 03 17:24:49 2017 -0400 +++ b/hubArchiveCreator.xml Mon Jul 10 17:06:11 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.1"> +<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.4.2"> <description> This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. @@ -222,8 +222,8 @@ <when value="bed"> <conditional name="bedChoice"> <param name="bed_select" type="select" label="Bed Choice"> - <option value="bed_generic" selected="true">BED Generic (bed3+)</option> - <option value="bed_cytoBand">cytoBand Track (bed4)</option> + <option value="bed_generic" selected="true">BED Generic (bed4)</option> + <option value="bed_cytoBand">cytoBand Track (bed4+1)</option> <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
--- a/templates/trackDb/layout.txt Mon Jul 03 17:24:49 2017 -0400 +++ b/templates/trackDb/layout.txt Mon Jul 10 17:06:11 2017 -0400 @@ -30,15 +30,23 @@ % if "NCBI" in trackDb.database: url https://www.ncbi.nlm.nih.gov/protein/$$ urlLabel ${trackDb.database} Details: +iframeUrl https://www.ncbi.nlm.nih.gov/protein/$$ +iframeOptions height='600' width='800' % elif "UniProt" in trackDb.database: url http://www.uniprot.org/uniprot/$$ urlLabel ${trackDb.database} Details: +iframeUrl http://www.uniprot.org/uniprot/$$ +iframeOptions height='600' width='800' % elif "FlyBase" in trackDb.database: url http://flybase.org/reports/$$ urlLabel ${trackDb.database} Details: +iframeUrl http://flybase.org/reports/$$ +iframeOptions height='600' width='800' % else: url https://www.ncbi.nlm.nih.gov/gquery/?term=$$ urlLabel NCBI Details: +iframeUrl https://www.ncbi.nlm.nih.gov/gquery/?term=$$ +iframeOptions height='600' width='800' % endif % elif "bigPsl" in trackDb.trackType and trackDb.database: @@ -57,9 +65,13 @@ % if "NCBI" in trackDb.database: url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Details: +iframeUrl https://www.ncbi.nlm.nih.gov/nuccore/$$ +iframeOptions height='600' width='800' % else: url https://www.ncbi.nlm.nih.gov/gquery/?term=$$ urlLabel NCBI Details: +iframeUrl https://www.ncbi.nlm.nih.gov/gquery/?term=$$ +iframeOptions height='600' width='800' % endif % else: