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Merge pull request #5254 from gregvonkuster/pt_datatypes2
Comment PlantTribes datatypes
This commit is contained in:
Martin Cech
@@ -631,18 +631,27 @@
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<datatype extension="maskinfo-asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" subclass="true" display_in_upload="true" />
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<datatype extension="pssm-asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" subclass="true" display_in_upload="true" />
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<!-- PlantTribes datatypes -->
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<!--
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The commented entries in this section are required by versions 1.0.0, 1.0.1 and 1.0.2 of the
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PlantTribes tools in the MTS Phylogenetics category, and are not required by version 1.0.3 of
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later. These datatypes will be removed in a future Galaxy release.
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-->
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<!--
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<datatype extension="ptalign" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment" />
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<datatype extension="ptalignca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment" />
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<datatype extension="ptaligntrimmed" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed" />
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<datatype extension="ptaligntrimmedca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment" />
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<datatype extension="ptalignfiltered" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered" />
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<datatype extension="ptalignfilteredca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment" />
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-->
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<datatype extension="ptkscmp" type="galaxy.datatypes.plant_tribes:PlantTribesKsComponents" display_in_upload="true"/>
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<!--
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<datatype extension="ptortho" type="galaxy.datatypes.plant_tribes:PlantTribesOrtho" />
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<datatype extension="ptorthocs" type="galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence" />
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<datatype extension="ptphylip" type="galaxy.datatypes.plant_tribes:PlantTribesPhylip" />
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<datatype extension="pttgf" type="galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies" />
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<datatype extension="pttree" type="galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree" />
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-->
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<datatype extension="smat" type="galaxy.datatypes.plant_tribes:Smat" display_in_upload="true" />
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<!-- Start Haplotype / LOD Datatypes -->
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<datatype extension="alohomora_gts" type="galaxy.datatypes.genetics:GenotypeMatrix" />
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@@ -1,12 +1,10 @@
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import logging
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import os
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import re
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from galaxy.datatypes.data import get_file_peek, Text
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from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
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from galaxy.datatypes.metadata import MetadataElement
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from galaxy.datatypes.sniff import get_headers
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from galaxy.datatypes.tabular import Tabular
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from galaxy.datatypes.text import Html
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from galaxy.util import nice_size
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log = logging.getLogger(__name__)
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@@ -75,20 +73,24 @@ class Smat(Text):
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return True
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class PlantTribes(Html):
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"""
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PlantTribes abstract class.
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"""
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composite_type = 'basic'
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MetadataElement(name="num_files", default=0, desc="Number of files in files_path directory", param=MetadataParameter, readonly=True, visible=False, no_value=0)
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def set_meta(self, dataset, overwrite=True, **kwd):
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try:
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efp = dataset.extra_files_path
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if os.path.exists(efp):
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dataset.metadata.num_files = len(os.listdir(efp))
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except Exception as e:
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log.warning("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
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# These commented classes are required by versions 1.0.0, 1.0.1 and 1.0.2 of the
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# PlantTribes tools in the MTS Phylogenetics category, and are not required by
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# version 1.0.3 or later. These datatypes will be removed in a future Galaxy release.
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#
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# class PlantTribes(Html):
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# """
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# PlantTribes abstract class.
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# """
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# composite_type = 'basic'
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# MetadataElement(name="num_files", default=0, desc="Number of files in files_path directory", param=MetadataParameter, readonly=True, visible=False, no_value=0)
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#
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# def set_meta(self, dataset, overwrite=True, **kwd):
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# try:
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# efp = dataset.extra_files_path
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# if os.path.exists(efp):
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# dataset.metadata.num_files = len(os.listdir(efp))
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# except Exception as e:
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# log.warning("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
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class PlantTribesKsComponents(Tabular):
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@@ -150,126 +152,125 @@ class PlantTribesKsComponents(Tabular):
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except Exception:
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return False
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class PlantTribesOrtho(PlantTribes):
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"""
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PlantTribes sequences classified into precomputed, orthologous gene family
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clusters.
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"""
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file_ext = "ptortho"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesOrtho, self).set_peek(dataset)
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dataset.blurb = "Proteins orthogroup fasta files: %d items" % dataset.metadata.num_files
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class PlantTribesOrthoCodingSequence(PlantTribes):
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"""
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PlantTribes sequences classified into precomputed, orthologous gene family
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clusters and corresponding coding sequences.
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"""
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file_ext = "ptorthocs"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesOrthoCodingSequence, self).set_peek(dataset)
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dataset.blurb = "Protein and coding sequences orthogroup fasta files: %d items" % dataset.metadata.num_files
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class PlantTribesTargetedGeneFamilies(PlantTribes):
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"""
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PlantTribes targeted gene families.
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"""
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file_ext = "pttgf"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesTargetedGeneFamilies, self).set_peek(dataset)
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dataset.blurb = "Targeted gene families"
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class PlantTribesPhylogeneticTree(PlantTribes):
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"""
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PlantTribes multiple sequence alignments and inferred maximum likelihood
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phylogenies for orthogroups.
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"""
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file_ext = "pttree"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesPhylogeneticTree, self).set_peek(dataset)
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dataset.blurb = "Phylogenetic trees: %d items" % dataset.metadata.num_files
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class PlantTribesPhylip(PlantTribes):
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"""
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PlantTribes orthogroup phylip multiple sequence alignments.
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"""
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file_ext = "ptphylip"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesPhylip, self).set_peek(dataset)
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dataset.blurb = "Orthogroup phylip multiple sequence alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignment(PlantTribes):
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"""
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PlantTribes multiple sequence alignments.
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"""
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file_ext = "ptalign"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset)
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dataset.blurb = "Proteins orthogroup alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignmentCodonAlignment(PlantTribes):
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"""
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PlantTribes multiple sequence alignments with codon alignments.
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"""
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file_ext = "ptalignca"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignmentCodonAlignment, self).set_peek(dataset)
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dataset.blurb = "Protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignmentTrimmed(PlantTribes):
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"""
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PlantTribes trimmed multiple sequence alignments.
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"""
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file_ext = "ptaligntrimmed"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignmentTrimmed, self).set_peek(dataset)
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dataset.blurb = "Trimmed proteins orthogroup alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment(PlantTribes):
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"""
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PlantTribes trimmed multiple sequence alignments with codon alignments.
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"""
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file_ext = "ptaligntrimmedca"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment, self).set_peek(dataset)
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dataset.blurb = "Trimmed protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignmentFiltered(PlantTribes):
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"""
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PlantTribes filtered multiple sequence alignments.
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"""
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file_ext = "ptalignfiltered"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignmentFiltered, self).set_peek(dataset)
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dataset.blurb = "Filtered proteins orthogroup alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment(PlantTribes):
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"""
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PlantTribes filtered multiple sequence alignments with codon alignments.
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"""
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file_ext = "ptalignfilteredca"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment, self).set_peek(dataset)
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dataset.blurb = "Filtered protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
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# class PlantTribesOrtho(PlantTribes):
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# """
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# PlantTribes sequences classified into precomputed, orthologous gene family
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# clusters.
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# """
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# file_ext = "ptortho"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesOrtho, self).set_peek(dataset)
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# dataset.blurb = "Proteins orthogroup fasta files: %d items" % dataset.metadata.num_files
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#
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#
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# class PlantTribesOrthoCodingSequence(PlantTribes):
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# """
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# PlantTribes sequences classified into precomputed, orthologous gene family
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# clusters and corresponding coding sequences.
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# """
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# file_ext = "ptorthocs"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesOrthoCodingSequence, self).set_peek(dataset)
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# dataset.blurb = "Protein and coding sequences orthogroup fasta files: %d items" % dataset.metadata.num_files
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#
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#
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# class PlantTribesTargetedGeneFamilies(PlantTribes):
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# """
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# PlantTribes targeted gene families.
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# """
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# file_ext = "pttgf"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesTargetedGeneFamilies, self).set_peek(dataset)
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# dataset.blurb = "Targeted gene families"
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#
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#
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# class PlantTribesPhylogeneticTree(PlantTribes):
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# """
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# PlantTribes multiple sequence alignments and inferred maximum likelihood
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# phylogenies for orthogroups.
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# """
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# file_ext = "pttree"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesPhylogeneticTree, self).set_peek(dataset)
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# dataset.blurb = "Phylogenetic trees: %d items" % dataset.metadata.num_files
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#
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#
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# class PlantTribesPhylip(PlantTribes):
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# """
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# PlantTribes orthogroup phylip multiple sequence alignments.
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# """
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# file_ext = "ptphylip"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesPhylip, self).set_peek(dataset)
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# dataset.blurb = "Orthogroup phylip multiple sequence alignments: %d items" % dataset.metadata.num_files
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#
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#
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# class PlantTribesMultipleSequenceAlignment(PlantTribes):
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# """
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# PlantTribes multiple sequence alignments.
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# """
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# file_ext = "ptalign"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset)
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# dataset.blurb = "Proteins orthogroup alignments: %d items" % dataset.metadata.num_files
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#
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#
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# class PlantTribesMultipleSequenceAlignmentCodonAlignment(PlantTribes):
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# """
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# PlantTribes multiple sequence alignments with codon alignments.
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# """
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# file_ext = "ptalignca"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesMultipleSequenceAlignmentCodonAlignment, self).set_peek(dataset)
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# dataset.blurb = "Protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
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#
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#
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# class PlantTribesMultipleSequenceAlignmentTrimmed(PlantTribes):
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# """
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# PlantTribes trimmed multiple sequence alignments.
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# """
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# file_ext = "ptaligntrimmed"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesMultipleSequenceAlignmentTrimmed, self).set_peek(dataset)
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# dataset.blurb = "Trimmed proteins orthogroup alignments: %d items" % dataset.metadata.num_files
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#
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#
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# class PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment(PlantTribes):
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# """
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# PlantTribes trimmed multiple sequence alignments with codon alignments.
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# """
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# file_ext = "ptaligntrimmedca"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment, self).set_peek(dataset)
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# dataset.blurb = "Trimmed protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
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#
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#
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# class PlantTribesMultipleSequenceAlignmentFiltered(PlantTribes):
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# """
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# PlantTribes filtered multiple sequence alignments.
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# """
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# file_ext = "ptalignfiltered"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesMultipleSequenceAlignmentFiltered, self).set_peek(dataset)
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# dataset.blurb = "Filtered proteins orthogroup alignments: %d items" % dataset.metadata.num_files
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#
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#
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# class PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment(PlantTribes):
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# """
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# PlantTribes filtered multiple sequence alignments with codon alignments.
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# """
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# file_ext = "ptalignfilteredca"
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#
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# def set_peek(self, dataset, is_multi_byte=False):
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# super(PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment, self).set_peek(dataset)
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# dataset.blurb = "Filtered protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
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