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https://github.com/galaxyproject/galaxy.git
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initial files by IyadKandalaft
This commit is contained in:
Iyad Kandalaft
committed by
shiltemann
shiltemann
parent
d9177a81e5
commit
3e5505fa4d
@@ -490,6 +490,45 @@
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<datatype extension="obfs" type="galaxy.datatypes.molecules:OBFS" mimetype="text/html" display_in_upload="False" />
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<datatype extension="phar" type="galaxy.datatypes.molecules:PHAR" display_in_upload="False" />
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<datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="True" />
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<!-- mothur formats -->
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<datatype extension="otu" type="galaxy.datatypes.mothur:Otu" display_in_upload="true"/>
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<datatype extension="list" type="galaxy.datatypes.mothur:Otu" subclass="True" display_in_upload="true"/>
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<datatype extension="sabund" type="galaxy.datatypes.mothur:Sabund" display_in_upload="true"/>
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<datatype extension="rabund" type="galaxy.datatypes.mothur:Sabund" subclass="True" display_in_upload="true"/>
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<datatype extension="shared" type="galaxy.datatypes.mothur:GroupAbund" subclass="True" display_in_upload="true"/>
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<datatype extension="relabund" type="galaxy.datatypes.mothur:GroupAbund" subclass="True" display_in_upload="true"/>
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<datatype extension="names" type="galaxy.datatypes.mothur:Names" display_in_upload="true"/>
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<datatype extension="design" type="galaxy.datatypes.mothur:Group" subclass="True" display_in_upload="true"/>
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<datatype extension="summary" type="galaxy.datatypes.mothur:Summary" display_in_upload="true"/>
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<datatype extension="groups" type="galaxy.datatypes.mothur:Group" display_in_upload="true"/>
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<datatype extension="oligos" type="galaxy.datatypes.mothur:Oligos" display_in_upload="true"/>
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<datatype extension="align" type="galaxy.datatypes.mothur:SequenceAlignment" display_in_upload="true"/>
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<datatype extension="accnos" type="galaxy.datatypes.mothur:AccNos" display_in_upload="true"/>
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<datatype extension="otulabels" type="galaxy.datatypes.mothur:AccNos" display_in_upload="true"/>
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<datatype extension="otu.corr" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true"/>
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<datatype extension="map" type="galaxy.datatypes.mothur:SecondaryStructureMap" display_in_upload="true"/>
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<datatype extension="align.check" type="galaxy.datatypes.mothur:AlignCheck" display_in_upload="true"/>
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<datatype extension="align.report" type="galaxy.datatypes.mothur:AlignReport" display_in_upload="true"/>
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<datatype extension="filter" type="galaxy.datatypes.mothur:LaneMask" display_in_upload="true"/>
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<datatype extension="dist" type="galaxy.datatypes.mothur:DistanceMatrix" display_in_upload="true"/>
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<datatype extension="pair.dist" type="galaxy.datatypes.mothur:PairwiseDistanceMatrix" display_in_upload="true"/>
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<datatype extension="square.dist" type="galaxy.datatypes.mothur:SquareDistanceMatrix" display_in_upload="true"/>
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<datatype extension="lower.dist" type="galaxy.datatypes.mothur:LowerTriangleDistanceMatrix" display_in_upload="true"/>
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<datatype extension="ref.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" display_in_upload="true">
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<converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="seq.taxonomy"/>
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</datatype>
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<datatype extension="seq.taxonomy" type="galaxy.datatypes.mothur:SequenceTaxonomy" display_in_upload="true"/>
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<datatype extension="rdp.taxonomy" type="galaxy.datatypes.mothur:RDPSequenceTaxonomy" display_in_upload="true"/>
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<datatype extension="cons.taxonomy" type="galaxy.datatypes.mothur:ConsensusTaxonomy" display_in_upload="true"/>
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<datatype extension="tax.summary" type="galaxy.datatypes.mothur:TaxonomySummary" display_in_upload="true"/>
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<datatype extension="freq" type="galaxy.datatypes.mothur:Frequency" display_in_upload="true"/>
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<datatype extension="quan" type="galaxy.datatypes.mothur:Quantile" display_in_upload="true"/>
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<datatype extension="filtered.quan" type="galaxy.datatypes.mothur:Quantile" subclass="True" display_in_upload="true"/>
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<datatype extension="masked.quan" type="galaxy.datatypes.mothur:Quantile" subclass="True" display_in_upload="true"/>
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<datatype extension="filtered.masked.quan" type="galaxy.datatypes.mothur:Quantile" subclass="True" display_in_upload="true"/>
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<datatype extension="axes" type="galaxy.datatypes.mothur:Axes" display_in_upload="true"/>
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<datatype extension="sff.flow" type="galaxy.datatypes.mothur:SffFlow" display_in_upload="true"/>
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<datatype extension="count_table" type="galaxy.datatypes.mothur:CountTable" display_in_upload="true"/>
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</registration>
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<sniffers>
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<!--
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@@ -499,6 +538,25 @@
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defined format first, followed by next-most rigidly defined,
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and so on.
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-->
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<sniffer type="galaxy.datatypes.mothur:Otu"/>
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<sniffer type="galaxy.datatypes.mothur:Sabund"/>
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<sniffer type="galaxy.datatypes.mothur:GroupAbund"/>
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<sniffer type="galaxy.datatypes.mothur:SharedRabund"/>
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<sniffer type="galaxy.datatypes.mothur:RelAbund"/>
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<sniffer type="galaxy.datatypes.mothur:SecondaryStructureMap"/>
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<sniffer type="galaxy.datatypes.mothur:SequenceAlignment"/>
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<sniffer type="galaxy.datatypes.mothur:LowerTriangleDistanceMatrix"/>
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<sniffer type="galaxy.datatypes.mothur:SquareDistanceMatrix"/>
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<sniffer type="galaxy.datatypes.mothur:PairwiseDistanceMatrix"/>
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<sniffer type="galaxy.datatypes.mothur:Oligos"/>
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<sniffer type="galaxy.datatypes.mothur:Frequency"/>
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<sniffer type="galaxy.datatypes.mothur:Quantile"/>
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<sniffer type="galaxy.datatypes.mothur:LaneMask"/>
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<sniffer type="galaxy.datatypes.mothur:RefTaxonomy"/>
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<sniffer type="galaxy.datatypes.mothur:SequenceTaxonomy"/>
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<sniffer type="galaxy.datatypes.mothur:RDPSequenceTaxonomy"/>
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<sniffer type="galaxy.datatypes.mothur:Phylip"/>
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<sniffer type="galaxy.datatypes.mothur:Axes"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyAscii"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyBinary"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkAscii"/>
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@@ -0,0 +1,31 @@
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#!/usr/bin/env python
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"""
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convert a ref.taxonommy file to a seq.taxonomy file
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Usage:
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%python ref_to_seq_taxonomy_converter.py <ref.taxonommy_filename> <seq.taxonomy_filename>
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"""
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import sys, os, re
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from math import *
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assert sys.version_info[:2] >= ( 2, 4 )
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def stop_err( msg ):
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sys.stderr.write( "%s" % msg )
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sys.exit()
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def __main__():
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infile_name = sys.argv[1]
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outfile = open( sys.argv[2], 'w' )
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pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)]))*(;)?)$'
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for i, line in enumerate( file( infile_name ) ):
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line = line.rstrip() # eliminate trailing space and new line characters
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if not line or line.startswith( '#' ):
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continue
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fields = line.split('\t')
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# make sure the 2nd field (taxonomy) ends with a ;
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outfile.write('%s\t%s;\n' % (fields[0], re.sub(';$','',fields[1])))
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outfile.close()
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if __name__ == "__main__": __main__()
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@@ -0,0 +1,12 @@
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<tool id="CONVERTER_ref_to_seq_taxomony" name="Convert Ref taxonomy to Seq Taxonomy" version="1.0.0">
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<description>converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format</description>
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<command interpreter="python">ref_to_seq_taxonomy_converter.py $input $output</command>
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<inputs>
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<param name="input" type="data" format="ref.taxonomy" label="a Sequence Taxomony file"/>
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</inputs>
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<outputs>
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<data name="output" format="seq.taxonomy"/>
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</outputs>
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<help>
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</help>
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</tool>
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