Mercurial > repos > jjohnson > snpsift_dbnsfp_datatypes
changeset 1:df236b5e2985 default tip
Change reference to extra_files_path
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 23 Oct 2014 05:53:39 -0500 |
| parents | 8a04c5e6bfe3 |
| children | |
| files | lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml lib/galaxy/datatypes/snpsift_dbnsfp.py |
| diffstat | 2 files changed, 2 insertions(+), 4 deletions(-) [+] |
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--- a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml Tue Oct 14 14:27:38 2014 -0400 +++ b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml Thu Oct 23 05:53:39 2014 -0500 @@ -1,6 +1,6 @@ <tool id="tabular_to_dbnsfp" name="Convert tabular to dbnsfp" version="1.0.0"> <description></description> - <command interpreter="python">tabular_to_dbnsfp.py $input $dbnsfp.dataset.extra_files_path/dbNSFP.gz</command> + <command interpreter="python">tabular_to_dbnsfp.py $input $dbnsfp.extra_files_path/dbNSFP.gz</command> <inputs> <param format="tabular" name="input" type="data" label="Choose a dbnsfp tabular file"/> </inputs>
--- a/lib/galaxy/datatypes/snpsift_dbnsfp.py Tue Oct 14 14:27:38 2014 -0400 +++ b/lib/galaxy/datatypes/snpsift_dbnsfp.py Thu Oct 23 05:53:39 2014 -0500 @@ -11,7 +11,7 @@ class SnpSiftDbNSFP( Text ): """Class describing a dbNSFP database prepared fpr use by SnpSift dbnsfp """ - MetadataElement( name='reference_name', default='dbSNFP' , desc='Reference Name', readonly=False, visible=True, set_in_upload=True, no_value='dbSNFP' ) + MetadataElement( name='reference_name', default='dbSNFP' , desc='Reference Name', readonly=True, visible=True, set_in_upload=True, no_value='dbSNFP' ) MetadataElement( name="bgzip", default=None, desc="dbNSFP bgzip", readonly=True, visible=True, no_value=None ) MetadataElement( name="index", default=None, desc="Tabix Index File", readonly=True, visible=True, no_value=None) MetadataElement( name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[] ) @@ -55,12 +55,10 @@ f.close() def set_meta( self, dataset, overwrite=True, **kwd ): try: - # Text.set_meta( self, dataset, **kwd) efp = dataset.extra_files_path if os.path.exists(efp): flist = os.listdir(efp) for i,fname in enumerate(flist): - # log.info("set_meta fname: %d %s" % (i,fname)) if fname.endswith('.gz'): dataset.metadata.bgzip = fname try: