Mercurial > repos > miller-lab > genome_diversity
changeset 25:cba0d7a63b82
workaround for gd_genotype datatype
admix shift int -> float
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Wed, 29 May 2013 13:49:19 -0400 |
| parents | 248b06e86022 |
| children | 91e835060ad2 |
| files | datatypes_conf.xml dpmix.xml lib/galaxy/datatypes/wsf.py |
| diffstat | 3 files changed, 6 insertions(+), 2 deletions(-) [+] |
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--- a/datatypes_conf.xml Tue May 28 16:24:19 2013 -0400 +++ b/datatypes_conf.xml Wed May 29 13:49:19 2013 -0400 @@ -7,7 +7,7 @@ <datatype extension="gd_indivs" type="galaxy.datatypes.wsf:Individuals" display_in_upload="true"/> <datatype extension="gd_ped" type="galaxy.datatypes.wsf:Wped" display_in_upload="true"/> <datatype extension="gd_snp" type="galaxy.datatypes.wsf:GDSnp" display_in_upload="true"/> - <datatype extension="gd_genotype" type="galaxy.datatypes.wsf:GDSnp" subclass="true" display_in_upload="true"/> + <datatype extension="gd_genotype" type="galaxy.datatypes.wsf:GDGenotype" display_in_upload="true"/> <datatype extension="gd_sap" type="galaxy.datatypes.wsf:GDSap" display_in_upload="true"/> <datatype extension="gd_covered_cds" type="galaxy.datatypes.interval:Interval" subclass="true" display_in_upload="true"/> </registration>
--- a/dpmix.xml Tue May 28 16:24:19 2013 -0400 +++ b/dpmix.xml Wed May 29 13:49:19 2013 -0400 @@ -42,7 +42,7 @@ <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" /> <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" /> - <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/> + <param name="switch_penalty" type="float" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/> </inputs> <outputs>
--- a/lib/galaxy/datatypes/wsf.py Tue May 28 16:24:19 2013 -0400 +++ b/lib/galaxy/datatypes/wsf.py Wed May 29 13:49:19 2013 -0400 @@ -176,6 +176,10 @@ dataset.metadata.individual_names = individual_names[:] dataset.metadata.individual_columns = individual_columns[:] +class GDGenotype( GDSnp ): + """ Webb's genotype file format """ + file_ext = 'gd_genotype' + class GDSap( Fake ): """ Webb's SAP file format """ file_ext = 'gd_sap'