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changeset 5:9d25b0fd882b

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Add cuffdatadb datatype (cummeRbund SQLite DB) to cuffdata.py
author Jim Johnson <jj@umn.edu>
date Tue, 09 Oct 2012 07:43:58 -0500
parents 77ca14d2bb3d
children 79c687de829b
files cuffdata.py cuffdata_datasets.xml cuffdiff_wrapper.xml cummerbund_wrapper.xml datatypes_conf.xml
diffstat 5 files changed, 10 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/cuffdata.py	Mon Oct 08 16:20:35 2012 -0500
+++ b/cuffdata.py	Tue Oct 09 07:43:58 2012 -0500
@@ -5,6 +5,7 @@
 import os,os.path,re
 import galaxy.datatypes.data
 from galaxy.datatypes.images import Html
+from galaxy.datatypes.binary import Binary
 from galaxy import util
 from galaxy.datatypes.metadata import MetadataElement
 
@@ -36,7 +37,7 @@
     tss_groups.read_group_tracking
     """
     file_ext = 'cuffdata'
-    is_binary = True
+    is_binary = False
     composite_type = 'auto_primary_file'
     allow_datatype_change = False
 
@@ -71,3 +72,7 @@
     def sniff( self, filename ):
         return False
 
+class CuffDataDB( Binary ):
+    file_ext = 'cuffdata'
+    is_binary = True
+    allow_datatype_change = False
--- a/cuffdata_datasets.xml	Mon Oct 08 16:20:35 2012 -0500
+++ b/cuffdata_datasets.xml	Tue Oct 09 07:43:58 2012 -0500
@@ -1,4 +1,4 @@
-<tool id="cuffdata_datasets" name="Cuffdata datasets" version="0.0.5">
+<tool id="cuffdata_datasets" name="Cuffdata datasets" version="0.0.6">
     <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 -->
     <description>history datasets from Cuffdiff output</description>
     <requirements>
--- a/cuffdiff_wrapper.xml	Mon Oct 08 16:20:35 2012 -0500
+++ b/cuffdiff_wrapper.xml	Tue Oct 09 07:43:58 2012 -0500
@@ -1,4 +1,4 @@
-<tool id="cuffdiff" name="Cuffdiff" version="0.0.5">
+<tool id="cuffdiff" name="Cuffdiff" version="0.0.6">
     <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 -->
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
     <requirements>
--- a/cummerbund_wrapper.xml	Mon Oct 08 16:20:35 2012 -0500
+++ b/cummerbund_wrapper.xml	Tue Oct 09 07:43:58 2012 -0500
@@ -1,4 +1,4 @@
-<tool id="cummerbund" name="cummeRbund" version="0.0.4">
+<tool id="cummerbund" name="cummeRbund" version="0.0.6">
     
     <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description>
     
--- a/datatypes_conf.xml	Mon Oct 08 16:20:35 2012 -0500
+++ b/datatypes_conf.xml	Tue Oct 09 07:43:58 2012 -0500
@@ -7,7 +7,7 @@
       <!-- composite dataset with cuffdiff outputs in the extra files path -->
       <datatype extension="cuffdata" type="galaxy.datatypes.cuffdata:CuffDiffData"/>
       <!-- SQLite database -->
-      <datatype extension="cuffdatadb" type="galaxy.datatypes.binary.Binary" subclass="true"/>
+      <datatype extension="cuffdatadb" type="galaxy.datatypes.cuffdata.CuffDataDB"/>
     </registration>
 </datatypes>