# HG changeset patch
# User bornea
# Date 1460989411 14400
# Node ID f2102787b4ff0fdcc5d5e710ae9c6bc1d29dd725
# Parent  9a110e634afeb885e255b796f89d70a0a2ac9aff
Uploaded

diff -r 9a110e634afe -r f2102787b4ff SAINT_preprocessing.xml
--- a/SAINT_preprocessing.xml	Mon Apr 18 10:21:10 2016 -0400
+++ b/SAINT_preprocessing.xml	Mon Apr 18 10:23:31 2016 -0400
@@ -80,21 +80,18 @@
 
 --------------
 
-1) MaxQuant or Scaffold
-^^^^^^^^^^^^^^^^^^^^^^^
+*1) MaxQuant or Scaffold*
 
 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. Please designate which one is being provided.
 
-2) Scaffold or MaxQuant File Input
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+*2) Scaffold or MaxQuant File Input*
 
 Select the corresponding *Samples Report* or *peptides.txt* here.
 
-3) Create Prey File
-^^^^^^^^^^^^^^^^^^^
+*3) Create Prey File*
 
 Select whether or not you would like APOSTL to generate a prey file.
 
@@ -107,8 +104,7 @@
 off in order to save time by circumventing this step as the same prey
 file can be used for both SAINTexpress runs.
 
-4) Provide Uniprot FASTA database
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+*4) Provide Uniprot FASTA database*
 
 Please specify a FASTA file containing the protein sequence. You can
 download the latest release of Uniprot's reviewed sequences (Swiss-Prot)
@@ -117,16 +113,14 @@
 generally advised to use the same FASTA database that was used for your
 database searches during peptide and protein ID.
 
-5) Are You Providing Your Own Bait File?
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+*5) Are You Providing Your Own Bait File?*
 
 Users have two options for providing a *Bait* file. If you would like to
 create your own *Bait* file, select Yes and designate the file below. If
 you would like to use the **Bait Create** tool to create a *Bait* file
 within Galaxy, please select No and proceed to the **Bait Create** tool.
 
-6) Bait File
-^^^^^^^^^^^^
+*6) Bait File*
 
 If you selected Yes above, please specify the *Bait* file you would like
 to provide. If you selected No above, ignore this argument and proceed
@@ -136,8 +130,7 @@
     within your Scaffold or MaxQuant output exactly and must contain no
     whitespace characters (e.g. spaces) or dashes.
 
-7) Bait Create
-^^^^^^^^^^^^^^
+*7) Bait Create*
 
 Using the **Bait Create** tool, you can create your *bait.txt* file.