changeset 2:b3cd322f7749

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 03 15:34:45 2014 -0400
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="installXena2" version="1.0">
+    <install version="1.0">
+      <actions>
+	<action type="set_environment">
+          <environment_variable name="XENA_BASE_DIR" action="set_to">$INSTALL_DIR/xena</environment_variable>
+        </action>
+      </actions>
+    </install>
+  </package>
+</tool_dependency>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xena_import.py	Wed Sep 03 15:34:45 2014 -0400
@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+
+"""
+  xena_import.py: import a dataset into Xena
+
+  Given a cmdline-specified genomic data file and a cmdline-specified Xena 
+  directory, import the genomic data fle into Xena.  This requires assembling
+  the necessary json file, based on cmdline input.
+"""
+
+import argparse
+import json
+import shutil
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("genomicDataPathname", type=str)
+    parser.add_argument("cohort", type=str)
+    parser.add_argument("type", type=str)
+    parser.add_argument("xenaInputDir", type=str)
+    args = parser.parse_args()
+
+    # Assemble the metadata in JSON format
+    metadata = { 'cohort': args.cohort, 'type': args.type }
+    jsonMetadata = json.dumps(metadata, indent=2) 
+    
+    # Write the metadata to a file in the Xena directory.  Use the filename
+    # of the genomic data file, with an added .json extension.
+    genomicDataFilename = args.genomicDataPathname.split("/")[-1]
+    jsonMetadataPathname = "%s/%s.json" % (args.xenaInputDir, 
+                                           genomicDataFilename)
+    fp = open(jsonMetadataPathname, "w")
+    fp.write("%s\n" % (jsonMetadata))
+    fp.close()
+
+    # Finally, copy the genomic data into the Xena directory
+    shutil.copy(args.genomicDataPathname, args.xenaInputDir)
+
+if __name__ == "__main__":
+    main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xena_import.xml	Wed Sep 03 15:34:45 2014 -0400
@@ -0,0 +1,17 @@
+<tool id="xenaImport" description="XENA Import" name="XENA Import" version="0.0.1">
+  <description>Import into the Xena VM</description>
+  <requirements>
+    <requirement type="package" version="1.0">installXena2</requirement>
+  </requirements>
+  <command interpreter="python">
+    xena_import.py ${xenaInputData} ${cohort} ${metadataType} ${XENA_BASE_DIR}/files/
+  </command>
+  <inputs>
+    <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>
+    <param format="str" type="text" name="cohort" label="Cohort" optional="false"/>
+    <param format="str" type="text" name="metadataType" label="Data Type (e.g. clinicalMatrix)" optional="false"/>
+  </inputs>
+  <help>
+    To Appear
+  </help>
+</tool>