diff metagene.xml @ 2:b2eb07000039

Fix spacing in environment_variables in tool_dependencies (breaks env.sh) Cleanup help sections.
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Tue, 21 Jul 2015 15:40:22 +0100
parents c34c364ce75d
children d7ce95ccf54f
line wrap: on
line diff
--- a/metagene.xml	Tue Jul 21 14:58:34 2015 +0100
+++ b/metagene.xml	Tue Jul 21 15:40:22 2015 +0100
@@ -148,18 +148,18 @@
 #. Select *Triplet periodicity (R data file)* from the previous step.
 
 #. Specify length of ribosome footprint reads to be used in filtering
-(lengths). Only these reads **will** be used in the analysis.
+   (lengths). Only these reads **will** be used in the analysis.
 
 #. Specify frames to consider. This information can be obtained
-from the *Triplet periodicity (HTML report)*.
+   from the *Triplet periodicity (HTML report)*.
 
-.. class:: warningmark
+   .. class:: warningmark
 
-Please note that the frames specified should correspond to the
-lengths of the reads.
+       Please note that the frames specified should correspond to the
+       lengths of the reads.
 
 #. Under *plotCDS parameters*, input length of footprints to be considered for
-generating the plot.
+   generating the plot.
 
 #. Review/change other options if necessary and execute program.
 
@@ -169,12 +169,12 @@
 
 #. Metagene analysis (HTML report)
 
-A HTML file with results and links to other output files - plots for
-specified lengths (PDF) and R script used for the session.
+   A HTML file with results and links to other output files - plots for
+   specified lengths (PDF) and R script used for the session.
 
 #. Metagene analysis (R data file)
 
-Used as input for the next step - *Plot Rribosome Profile*.
+   Used as input for the next step - *Plot Rribosome Profile*.
 
 riboSeqR functions used
 .......................