Mercurial > repos > melissacline > ucsc_xena_platform
changeset 18:154a9b440b63
Updated the xena jar to version 14, updated the URL of the Xena pages
| author | melissacline |
|---|---|
| date | Tue, 02 Jun 2015 14:55:55 -0700 |
| parents | 6785e729c7ad (current diff) c298bb05640e (diff) |
| children | 782e91e9ef48 |
| files | ucsc_xena_datapages.xml ucsc_xena_hub.xml ucsc_xenabrowser.xml xena.jar xena_utils.pyc |
| diffstat | 2 files changed, 9 insertions(+), 5 deletions(-) [+] |
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--- a/runXena.py Tue Jun 02 14:54:24 2015 -0700 +++ b/runXena.py Tue Jun 02 14:55:55 2015 -0700 @@ -34,7 +34,7 @@ while True: #Main code goes here ... #Note that logger level needs to be set to logging.DEBUG before this shows up in the logs - xenaCmdline = "java -jar %s -r %s/files -d %s/db -t %s/tmp --logfile %s/xena.log -p %s -H 0.0.0.0 --no-auto" + xenaCmdline = "java -jar %s -r %s/files -d %s/db -t %s/tmp --logfile %s/xena.log -p %s -H 0.0.0.0" xenaBaseDir = xena.baseDir() xenaCmd = xenaCmdline % (xena.jarPath(), xenaBaseDir, xenaBaseDir, xenaBaseDir,
--- a/xena_import.xml Tue Jun 02 14:54:24 2015 -0700 +++ b/xena_import.xml Tue Jun 02 14:55:55 2015 -0700 @@ -32,8 +32,8 @@ <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/> <conditional name="source"> <param type="select" name="metadataSource" label="Metadata entry"> + <option value="entry">Enter your own</option> <option value="json">Specify json metadata file</option> - <option value="entry">Enter your own</option> </param> <when value="json"> <param format="data" type="data" name="xenaMetadata" label="Metadata file" optional="false"/> @@ -42,8 +42,8 @@ <param format="str" type="text" name="cohort" label="Cohort" optional="false"/> <conditional name="format"> <param type="select" name="metadataType" label="File Format"> - <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples)</option> - <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers)</option> + <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples) (often genomic data)</option> + <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers) (often clinical data)</option> <option value="mutationVector">Mutation By Position</option> </param> <when value="genomicMatrix"> @@ -57,6 +57,7 @@ <option value="gene expression">gene expression</option> <option value="gene expression RNAseq">gene expression RNAseq</option> <option value="gene expression Array">gene expression Array</option> + <option value="mRNA expression">mRNA expression</option> <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option> <option value="somatic mutation (gene level)">somatic mutation (gene level)</option> <option value="protein expression RPPA">protein expression RPPA</option> @@ -72,6 +73,7 @@ <when value="gene expression"/> <when value="gene expression RNAseq"/> <when value="gene expression Array"/> + <when value="mRNA expression"/> <when value="somatic mutation (SNP and small INDELs)"/> <when value="somatic mutation (gene level)"/> <when value="protein expression RPPA"/> @@ -89,6 +91,7 @@ <option value="gene expression">gene expression</option> <option value="gene expression RNAseq">gene expression RNAseq</option> <option value="gene expression Array">gene expression Array</option> + <option value="mRNA expression">mRNA expression</option> <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option> <option value="somatic mutation (gene level)">somatic mutation (gene level)</option> <option value="protein expression RPPA">protein expression RPPA</option> @@ -104,6 +107,7 @@ <when value="gene expression"/> <when value="gene expression RNAseq"/> <when value="gene expression Array"/> + <when value="mRNA expression"/> <when value="somatic mutation (SNP and small INDELs)"/> <when value="somatic mutation (gene level)"/> <when value="protein expression RPPA"/> @@ -121,6 +125,6 @@ <data format="txt" name="outfile"/> </outputs> <help> - To Appear soon... + To Appear, soon... </help> </tool>