changeset 16:d0667be9cb0c draft

Uploaded

--- a/bamCorrelate.xml	Thu Nov 28 12:58:28 2013 -0500
+++ b/bamCorrelate.xml	Thu Nov 28 13:22:04 2013 -0500
@@ -15,14 +15,7 @@
 
         bamCorrelate
 
-        #if $mode.modeOpt == "bins":
-            bins
-            --binSize '$mode.binSize'
-            --numberOfSamples '$mode.numberOfSamples'
-        #else:
-            BED-file
-            --BED $mode.region_file
-        #end if
+        $mode.modeOpt
 
         @THREADS@
 
@@ -40,6 +33,13 @@
             --outFileCorMatrix '$outFileCorMatrix'
         #end if
 
+        #if $mode.modeOpt == "bins":
+            --binSize '$mode.binSize'
+            --numberOfSamples '$mode.numberOfSamples'
+        #else:
+            --BED $mode.region_file
+        #end if
+
         ## options available in both modes
         #if $mode.advancedOpt.showAdvancedOpt == "yes":
 

--- a/correctGCBias.xml	Thu Nov 28 12:58:28 2013 -0500
+++ b/correctGCBias.xml	Thu Nov 28 13:22:04 2013 -0500
@@ -16,6 +16,9 @@
 
 
   correctGCBias
+
+    @THREADS@
+
   --bamfile '$temp_bam_path'
   --GCbiasFrequenciesFile $GCbiasFrequenciesFile
 

--- a/readme.rst	Thu Nov 28 12:58:28 2013 -0500
+++ b/readme.rst	Thu Nov 28 13:22:04 2013 -0500
@@ -29,7 +29,7 @@
 Citation
 ========
 
-deeptools are currently under review. In the meantime please refere to
+deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
 
 
 =======
@@ -39,25 +39,23 @@
 - v1.0: Initial public release
 
 
-===============================
-Wrapper Licence (MIT/BSD style)
-===============================
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
 
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
-
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.