Mercurial > repos > melissacline > ucsc_xena_platform
changeset 49:8da6920a39ac
add hg19 assembly in xena_import
| author | jingchunzhu |
|---|---|
| date | Sun, 09 Aug 2015 23:23:58 -0700 |
| parents | d717d0c4c8f1 |
| children | 3167c1a26101 |
| files | xena_import.py xena_import.xml |
| diffstat | 2 files changed, 18 insertions(+), 5 deletions(-) [+] |
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--- a/xena_import.py Sun Aug 09 22:39:09 2015 -0700 +++ b/xena_import.py Sun Aug 09 23:23:58 2015 -0700 @@ -54,6 +54,7 @@ parser.add_argument("--label", type=str, default=None) parser.add_argument("--colNormalization", type=bool, default=False) parser.add_argument("--probeMap", type=str, default=None) + parser.add_argument("--assembly", type=str, default=None) args = parser.parse_args() fp2 = open(args.outfile, "w") @@ -90,7 +91,8 @@ updateColNormalization(metadata) if args.probeMap is not None: metadata[':probeMap'] = probeMapDataFile - + if args.assembly: + metadata['assembly'] = args.assembly jsonMetadata = json.dumps(metadata, indent=2) fp = open(jsonMetadataTargetPathname, "w") fp.write("%s\n" % (jsonMetadata))
--- a/xena_import.xml Sun Aug 09 22:39:09 2015 -0700 +++ b/xena_import.xml Sun Aug 09 23:23:58 2015 -0700 @@ -26,9 +26,14 @@ --probeMap "${format.withProbeMap.probeMapFile}" #end if - #if $colNormalization: + #if $format.metadataType == "genomicMatrix" and $format.colNormalization: --colNormalization 1 #end if + + #if $format.metadataType == "mutationVector" and $format.assembly: + --assembly "${format.assembly}" + #end if + </command> <inputs> <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/> @@ -81,8 +86,10 @@ <when value="protein expression RPPA"/> <when value="PARADIGM pathway activity"/> </conditional> - + + <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/> </when> + <when value="clinicalMatrix"> <conditional name="isCustom"> <param type="select" name="dataSubType" label="Type of data"> @@ -95,10 +102,14 @@ <when value="phenotype"/> </conditional> </when> - <when value="mutationVector"/> + + <when value="mutationVector"> + <param type="select" name="assembly" label ="assembly"> + <option value = "hg19"> hg19</option> + </param> + </when> </conditional> <param type="text" name="label" label="Display Name (Optional)" optional="true"/> - <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/> </inputs> <outputs> <data format="txt" name="outfile"/>