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Add RGenetic datatypes to datatypes.conf.sample and remove the always true sniff method of SNPMatrix

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Daniel Blankenberg
2008-12-01 13:24:01 -05:00
parent fd0636f356
commit c8a71a49f8
2 changed files with 28 additions and 4 deletions
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datatypes_conf.xml.sample
+24
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@@ -140,6 +140,30 @@
<datatype extension="wobble" type="galaxy.datatypes.data:Text"/>
<datatype extension="wordcount" type="galaxy.datatypes.data:Text"/>
<datatype extension="tagseq" type="galaxy.datatypes.data:Text"/>
<!-- Start RGenetics Datatypes -->
<!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
<datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
<datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
<!-- linkage format pedigree (separate .map file) -->
<datatype extension="lped" type="galaxy.datatypes.genetics:Lped"/>
<!-- plink compressed file - has bed extension unfortunately -->
<datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed"/>
<!-- eigenstrat pedigree input file -->
<datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
<!-- eigenstrat pca output file for adjusted eigenQTL eg -->
<datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
<!-- fbat/pbat format pedigree (header row of marker names) -->
<datatype extension="fped" type="galaxy.datatypes.genetics:Fped"/>
<!-- part of linkage format pedigree -->
<datatype extension="lmap" type="galaxy.datatypes.genetics:Lmap"/>
<!-- phenotype file - fbat format -->
<datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe"/>
<!-- phenotype file - plink format -->
<datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe"/>
<datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest"/>
<datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix"/>
<datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/>
<!-- End RGenetics Datatypes -->
</registration>
<sniffers>
<!--
lib/galaxy/datatypes/genetics.py
+4 -4
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@@ -132,10 +132,10 @@ class SNPMatrix(Rgenetics):
def set_peek( self, dataset ):
dataset.peek = "Binary RGenetics file"
dataset.blurb = data.nice_size( dataset.get_size() )
def sniff( self, filename ):
"""
"""
return True
#def sniff( self, filename ):
# """
# """
# return True
class Lped(Rgenetics):
"""fake class to distinguish different species of Rgenetics data collections