# HG changeset patch
# User bornea
# Date 1454020440 18000
# Node ID a9d2cab6a8ce85540c6f176bc6390974b72439c9
# Parent  fce21ee45396dbc0c0c1e85e684411deb344dc6c
Uploaded

diff -r fce21ee45396 -r a9d2cab6a8ce SAINT_preprocessing_v6.xml
--- a/SAINT_preprocessing_v6.xml	Thu Jan 28 13:54:09 2016 -0500
+++ b/SAINT_preprocessing_v6.xml	Thu Jan 28 17:34:00 2016 -0500
@@ -25,7 +25,6 @@
   </command>
   <requirements>
     <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
-    <requirement type="package" version="3.2.1">package_r_3_2_1</requirement>
   </requirements>
   <inputs>
     <param type="select" name="type" label="MaxQuant or Scaffold">
@@ -72,7 +71,7 @@
   </tests>
   <help>
 
-Pre-processing:
+**Pre-processing**
 
 APOSTL is able to recognize either a Scaffold "Samples Report" file (tab-delimited txt file) or the "peptides.txt" file output in the MaxQuant "txt" output folder. No modifications should be made to these files. Using the "Bait Create" tool, you can create your "bait.txt" file. It is important that the individual bait names match the bait names within your scaffold or MaxQuant output. APOSTL uses the bait file to findthe user's baits of interest. Additionally there is an option to make the prey file (Y/N). When making a prey file, APOSTL queries Uniprot ( http://www.uniprot.org ) in order to extract protein amino acidlengths and gene names. This takes several minutes depending on your internet connection. Some users may want to run SAINTexpress using the same data set while changing which baits are considered test or control It is useful to toggle "Make Prey" off in order to save time by circumventing this step as the same prey file can be used for both SAINTexpress runs. 
 
@@ -80,11 +79,10 @@
 
 Scaffold file:
 
-- Scaffold "Samples Report" output (tab-delimited txt file)
-
+Scaffold "Samples Report" output (tab-delimited txt file)
 
 MaxQuant file:
 
-- MaxQuant "peptides.txt" file (tab-delimited txt file)
+MaxQuant "peptides.txt" file (tab-delimited txt file)
   </help>
 </tool>