--- a/process_scans.xml	Sat Apr 11 16:48:19 2020 -0400
+++ b/process_scans.xml	Tue Apr 28 17:32:59 2020 -0400
@@ -7,8 +7,12 @@
     <command detect_errors="exit_code">
     <![CDATA[
         #if $data.input[0].is_of_type("zip")
+            dimspy unzip 
+            --input $data.input[0]
+            --output ./data
+            &&
             dimspy process-scans
-            --input $data.input[0]
+            --input ./data
         #else
             #for $fn in $data.input
                 ln -s '$fn' '$fn.name'
@@ -212,7 +216,7 @@
 Description
 -----------
 
-Standard DIMS processing workflow: **Process Scans** -> Replicate Filter -> Align Samples -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics
+Standard DIMS processing workflow: **Process Scans** -> [Replicate Filter] -> Align Samples -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> [Missing values sample filter] -> Pre-processing -> Statistics
 
 This tool is used to generate a single mass spectral peaklist for each of the data files defined in the ‘Filelist/Samplelist’. The tool extracts mass spectral peaks from a data file (in either .mzML or .RAW format) and then filters these in accordance with user-defined parameter settings. All peaks remaining after filtering are hierarchically clustered in one-dimension, during which pairs of peaks with similar m/z values are grouped together if the difference between their m/z values, when divided by the average of their m/z values and multiplied by 1 x 10\ :sup:`6` \, equates to less-than the user-defined ppm error tolerance.