diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index 59acb3c7c92..cb6e4f1fa13 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -598,6 +598,10 @@ + + + + diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py index ec55ea4cded..9399c026f43 100644 --- a/lib/galaxy/datatypes/text.py +++ b/lib/galaxy/datatypes/text.py @@ -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