# HG changeset patch
# User bornea
# Date 1472346072 14400
# Node ID 340cc5988c31e54d23dc9d529045223706748b83
# Parent 0f5028e0c39c843943592bd307c5f413bd0ecdb3
Uploaded
diff -r 0f5028e0c39c -r 340cc5988c31 SAINT_preprocessing.xml
--- a/SAINT_preprocessing.xml Sat Aug 27 20:25:34 2016 -0400
+++ b/SAINT_preprocessing.xml Sat Aug 27 21:01:12 2016 -0400
@@ -21,28 +21,71 @@
#end for
"
$Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in
+ #elif (str($type) == 'Peptideshaker'):
+ Protein_report_processing.py "$input" $Bait_file $use_metric $fasta_db $preybool
+ "
+ #for $ba in $bait
+ ${ba.bait1}
+ ${ba.assign}
+ ${ba.T_C}
+ #end for
+ "
+ \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in $Inter_file $Prey_file
#end if
INSTALL_RUN_PATH
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@@ -83,8 +126,9 @@
^^^^^^^^^^^^^^
This tool will read in a Scaffold *Samples Report* file (tab-delimited
-txt file) or a MaxQuant *peptides.txt* file and process them to generate
-a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis.
+txt file), multiple Peptideshaker *Protein Report* files or a MaxQuant
+*peptides.txt* file and process them to generate a *Bait File, Prey
+File,* and *Inter File* for SAINTexpress analysis.
--------------
@@ -137,6 +181,9 @@
**Note:** Individual bait names must match to the sample names
within your Scaffold or MaxQuant output exactly and must contain no
whitespace characters (e.g. spaces) or dashes.
+
+ **Note:** When using Peptideshaker output the baits in the baitfile
+ need to be in the same order as the files selected.
**7) Bait Create**