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Merge pull request #3698 from gregvonkuster/ptformats

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Add datatypes for soon coming PlantTribes Galaxy tools.
This commit is contained in:
Dannon Baker
2017-03-07 12:58:44 -05:00
committed by GitHub
parent 9ccb0953ad a7ec0c8579
commit 1b12259739
2 changed files with 51 additions and 0 deletions
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config/datatypes_conf.xml.sample
+4
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@@ -598,6 +598,10 @@
<datatype extension="maskinfo-asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" subclass="true" display_in_upload="true" />
<datatype extension="pssm-asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" subclass="true" display_in_upload="true" />
<!-- PlantTribes datatypes -->
<datatype extension="ptalign" type="galaxy.datatypes.text:PlantTribesMultipleSequenceAlignment" />
<datatype extension="ptortho" type="galaxy.datatypes.text:PlantTribesOrtho" />
<datatype extension="ptorthocs" type="galaxy.datatypes.text:PlantTribesOrthoCodingSequence" />
<datatype extension="pttree" type="galaxy.datatypes.text:PlantTribesPhylogeneticTree" />
<datatype extension="smat" type="galaxy.datatypes.text:Smat" display_in_upload="true" />
</registration>
<sniffers>
lib/galaxy/datatypes/text.py
+47
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@@ -605,3 +605,50 @@ class Smat(Text):
if re.match(r"[-+]?\d+$", item) is None:
return False
return True
class PlantTribesOrtho(Html):
"""
PlantTribes sequences classified into precomputed, orthologous gene family
clusters.
"""
file_ext = "ptortho"
def set_peek(self, dataset, is_multi_byte=False):
super(PlantTribesOrtho, self).set_peek(dataset, is_multi_byte=is_multi_byte)
dataset.blurb = "PlantTribes gene family clusters: %d files" % dataset.metadata.data_lines
class PlantTribesOrthoCodingSequence(Html):
"""
PlantTribes sequences classified into precomputed, orthologous gene family
clusters and corresponding coding sequences.
"""
file_ext = "ptorthocs"
def set_peek(self, dataset, is_multi_byte=False):
super(PlantTribesOrthoCodingSequence, self).set_peek(dataset, is_multi_byte=is_multi_byte)
dataset.blurb = "PlantTribes gene family clusters with corresponding coding sequences: %d files" % dataset.metadata.data_lines
class PlantTribesPhylogeneticTree(Html):
"""
PlantTribes multiple sequence alignments and inferred maximum likelihood
phylogenies for orthogroups.
"""
file_ext = "pttree"
def set_peek(self, dataset, is_multi_byte=False):
super(PlantTribesPhylogeneticTree, self).set_peek(dataset, is_multi_byte=is_multi_byte)
dataset.blurb = "PlantTribes phylogenetic trees: %d files" % dataset.metadata.data_lines
class PlantTribesMultipleSequenceAlignment(Html):
"""
PlantTribes multiple sequence alignments for orthogroups.
"""
file_ext = "ptalign"
def set_peek(self, dataset, is_multi_byte=False):
super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
dataset.blurb = "PlantTribes multiple sequence alignments: %d files" % dataset.metadata.data_lines