Recent changes to ChipsterToolConventions

ChipsterToolConventions modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:43:07 -0000

--- v2
+++ v3
@@ -1,22 +1 @@
-[TOC]
-
-## Conventions for Chipster analysis tools
-
-Here we describe different conventions that should be followed when developing or integrating tools to Chipster. The goal in Chipster is always to produce a coherent user experience, for which reason a lot of attention should be placed to harmonising the tools. 
-
-### Common conventions
-
-### Microarray analysis module
-
-  * The default data format is TSV (tab separated values), with one row for each gene or probeset 
-  * The first column should be unnamed or "identifier" and contain the gene/probeset name 
-  * Tool should not removed any existing columns unless the row structure is changed 
-    * In other words, inputs can have annotation etc. data that just passes through analysis steps 
-  * See AnalysisToolInputsAndOutputs for more information, in version 2.0 typing will be decided by the analysis module and will be described in this page 
-
-### Sequence analysis module
-
-### NGS analysis module
-
-  * Tools should accept and produce read data in BAM format 
-  * Tools should assume chromosome names to not have any prefices or suffices (so "12" instead of "chr12") 
+Moved to https://sourceforge.net/apps/mediawiki/chipster/index.php?title=TechnicalManual14#Conventions_for_Chipster_analysis_tools

ChipsterToolConventions modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:43:07 -0000

--- v1
+++ v2
@@ -2,19 +2,21 @@

 ## Conventions for Chipster analysis tools

+Here we describe different conventions that should be followed when developing or integrating tools to Chipster. The goal in Chipster is always to produce a coherent user experience, for which reason a lot of attention should be placed to harmonising the tools. 
+
 ### Common conventions

 ### Microarray analysis module
-    
-      * The default data format is TSV (tab separated values), with one row for each gene or probeset
-      * The first column should be unnamed or "identifier" and contain the gene/probeset name
-      * See AnalysisToolInputsAndOutputs for more information, in version 2.0 typing will be decided by the analysis module and will be described in this page
-    
+
+  * The default data format is TSV (tab separated values), with one row for each gene or probeset 
+  * The first column should be unnamed or "identifier" and contain the gene/probeset name 
+  * Tool should not removed any existing columns unless the row structure is changed 
+    * In other words, inputs can have annotation etc. data that just passes through analysis steps 
+  * See AnalysisToolInputsAndOutputs for more information, in version 2.0 typing will be decided by the analysis module and will be described in this page 

 ### Sequence analysis module

 ### NGS analysis module
-    
-      * Tools should accept and produce read data in BAM format
-      * Tools should assume chromosome names to not have any prefices or suffices (so "12" instead of "chr12")
-    
+
+  * Tools should accept and produce read data in BAM format 
+  * Tools should assume chromosome names to not have any prefices or suffices (so "12" instead of "chr12")

ChipsterToolConventions modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:43:07 -0000

Conventions for Chipster analysis tools

Conventions for Chipster analysis tools

Common conventions

Microarray analysis module

  * The default data format is TSV (tab separated values), with one row for each gene or probeset
  * The first column should be unnamed or "identifier" and contain the gene/probeset name
  * See AnalysisToolInputsAndOutputs for more information, in version 2.0 typing will be decided by the analysis module and will be described in this page

Sequence analysis module

NGS analysis module

  * Tools should accept and produce read data in BAM format
  * Tools should assume chromosome names to not have any prefices or suffices (so "12" instead of "chr12")