--- a/mqppep_anova.xml	Tue Mar 22 23:12:18 2022 +0000
+++ b/mqppep_anova.xml	Sat Mar 26 02:27:12 2022 +0000
@@ -22,7 +22,7 @@
       \${CONDA_PREFIX}/bin/Rscript \$TEMP/mqppep_anova.R
         --inputFile '$input_file'
         --alphaFile '$alpha_file'
-        --firstDataColumn $first_data_column
+        --firstDataColumn $intensity_column_regex_f
         --imputationMethod $imputation.imputation_method
         #if $imputation.imputation_method == "random"
           --meanPercentile '$imputation.meanPercentile'
@@ -45,6 +45,9 @@
       <configfile name="sample_grouping_regex_f">
         $sample_grouping_regex
       </configfile>
+      <configfile name="intensity_column_regex_f">
+        $intensity_column_regex
+      </configfile>
     </configfiles>
     <inputs>
         <param name="input_file" type="data" format="tabular" label="Filtered Phosphopeptide Intensities"
@@ -53,9 +56,9 @@
         <param name="alpha_file" type="data" format="tabular" label="alpha cutoff level"
                help="[alpha_file] List of alpha cutoff values for significance testing; text file having one column and no header"
         />
-        <param name="first_data_column" type="text" value="Intensity"
-               label="First data column"
-               help="[first_data_column] First column having intensity values (integer or PERL-compatible regular expression matching column label)"
+        <param name="intensity_column_regex" type="text" value="^Intensity[^_]"
+               label="Intensity-column pattern"
+               help="[intensity_column_regex] Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)"
         />
         <!-- imputation_method <- c("group-median","median","mean","random")[1] -->
         <conditional name="imputation">
@@ -75,15 +78,15 @@
                        label="Mean percentile for random values"
                        help="[meanPercentile] Percentile center of random values; range [1,99]"
                 />
-                <param name="sdPercentile" type="float" value="0.2"
+                <param name="sdPercentile" type="float" value="1.0"
                        label="Percentile std. dev. for random values"
                        help="[sdPercentile] Standard deviation adjustment-factor for random values; real number.  (1.0 means SD equal to the SD for the entire data set.)"
                 />
             </when>
         </conditional>
         <param name="sample_names_regex" type="text" value="\.\d+[A-Z]$"
-               help="[sample_names_regex] PERL-compatible regular expression extracting sample-names from the the name of a spectrum file (without extension)"
-               label="Sample-extraction regex">
+               help="[sample_names_regex] Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)"
+               label="Sample-extraction pattern">
           <sanitizer>
             <valid initial="string.printable">
               <remove value="&apos;"/>
@@ -91,8 +94,8 @@
           </sanitizer>
         </param>
         <param name="sample_grouping_regex" type="text" value="\d+"
-               help="[sample_grouping_regex] PERL-compatible regular expression extracting sample-group from each sample-name (i.e., extracted by previous regex pattern)"
-               label="Group-extraction regex">
+               help="[sample_grouping_regex] Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)"
+               label="Group-extraction pattern">
           <sanitizer>
             <valid initial="string.printable">
               <remove value="&apos;"/>
@@ -112,7 +115,7 @@
         <test>
             <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
             <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
-            <param name="first_data_column" value="10"/>
+            <param name="intensity_column_regex" value="^Intensity[^_]"/>
             <param name="imputation_method" value="group-median"/>
             <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
             <param name="sample_grouping_regex" value="\d+"/>
@@ -128,10 +131,10 @@
         <test>
             <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
             <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
-            <param name="first_data_column" value="10"/>
+            <param name="intensity_column_regex" value="^Intensity[^_]"/>
             <param name="imputation_method" value="random"/>
             <param name="meanPercentile" value="1" />
-            <param name="sdPercentile" value="0.2" />
+            <param name="sdPercentile" value="1.0" />
             <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
             <param name="sample_grouping_regex" value="\d+"/>
             <output name="imp_qn_lt_file">
@@ -167,7 +170,7 @@
 
 **Input parameters**
 
-``first_data_column``
+``intensity_column_regex``
   First column of ``input_file`` having intensity values (integer or PERL-compatible regular expression matching column label). Default: **Intensity**
 
 ``imputation_method``