--- a/preprocessing.xml	Wed Apr 19 22:46:23 2023 +0000
+++ b/preprocessing.xml	Thu Jul 04 13:38:14 2024 +0000
@@ -1,16 +1,11 @@
-<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1">
+<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>
         mass spectrometry imaging preprocessing
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.4.0">r-ggplot2</requirement>
-        <requirement type="package" version="3.40.0">bioconductor-sva</requirement>
-        <requirement type="package" version="1.1.0.1">r-randomcolor</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
     <![CDATA[
 
@@ -371,19 +366,19 @@
 
             #if str($method.methods_conditional.mz_range.features_filtering) == 'change_mz_range':
 
-                msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
+                msidata = mse_bin = mzBin(msidata, resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
 
 		   
 	    #elif str($method.methods_conditional.mz_range.features_filtering) == 'none':
 
-                msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
+                msidata = mse_bin = mzBin(msidata, resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
 
 	    #elif str($method.methods_conditional.mz_range.features_filtering) == 'bin_to_reference':
 
 	        bin_reference_mz = read.delim("$method.methods_conditional.mz_range.mz_tabular", header = $method.methods_conditional.mz_range.feature_header, stringsAsFactors = FALSE)
                 bin_reference_mz = bin_reference_mz[,$method.methods_conditional.mz_range.feature_column]
 
-	       msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun,
+	       msidata = mse_bin = mzBin(msidata, resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun",
 	       ref=bin_reference_mz)
 
             #end if
@@ -479,7 +474,7 @@
                         error=function(cond) {
                         ## in case user provided an annotation tabular with less than two batches
                             message("Error in annotation tabular")
-                            message("Possible problems: Annotation tabular file has not enough batch levels - to perform ComBat at least 2 batches and 2 pixels per batch are necessary)")
+                            message("Possible problems: Annotation tabular file has not enough batch levels - to perform ComBat at least 2 batches and 2 pixels per batch are necessary")
                             stop(call.=FALSE)
                         }
                     )
@@ -812,7 +807,7 @@
                 <when value="ComBat_batch_correction">
 		     <param name="annotation_file" type="data" format="tabular" label="Annotation file that contains the pixel x and y coordinates, the batch identifier, and the condition annotation for each spectrum." help="Annotation tabular file that contains the batch identifier for each spectrum in one column."/>
                        <param name="x_column" type="data_column" data_ref="annotation_file" label="X coordinates" help="Column with x coordinates of pixels."/>
-                       <param name="y_column" type="data_column" data_ref="annotation_file" label="Y coordinates" help="Column with y ccordinates of pixels."/>
+                       <param name="y_column" type="data_column" data_ref="annotation_file" label="Y coordinates" help="Column with y coordinates of pixels."/>
                        <param name="batch_column" type="data_column" data_ref="annotation_file" label="Batch column" help="The column that contains the batch identifier for each spectrum."/>
                        <param name="condition_column" type="data_column" data_ref="annotation_file" label="Condition column" help="The column that contains the condition annotation for each spectrum. Typically these are the groups you want to compare. If not applicable, the batch column can be selected again as this information is only used for the QC plot."/>
                        <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
@@ -955,7 +950,7 @@
                     <param name="alignment_units" value="ppm"/>
                     <param name="mz_tabular" value="inputcalibrantfile2.txt" ftype="tabular"/>
                     <param name="feature_column" value="1"/>
-                    <param name="feature_header" value="TRUE"/>
+                    <param name="feature_header" value="FALSE"/>
                 </conditional>
             </repeat>
             <repeat name="methods">
@@ -1023,7 +1018,7 @@
             <expand macro="processed_infile_imzml"/>
             <conditional name="processed_cond">
                 <param name="processed_file" value="processed"/>
-                <param name="accuracy" value="50"/>
+                <param name="accuracy" value="200"/>
                 <param name="units" value="ppm"/>
             </conditional>
             <repeat name="methods">   
@@ -1037,7 +1032,7 @@
                     <param name="condition_column" value="5"/>
                 </conditional>
             </repeat>
-            <output name="QC_overview" file="ComBat_results_Example_processed_file_preprocessing.pdf" compare="sim_size"/>
+            <output name="QC_overview" file="ComBat_results_Example_processed_file.pdf" compare="sim_size"/>
             <output name="outfile_imzml" ftype="imzml" file="ComBat_results_Example_processed_file.imzml.txt" compare="sim_size">
                 <extra_files type="file" file="ComBat_results_Example_processed_file.imzml" name="imzml" lines_diff="6"/>
                 <extra_files type="file" file="ComBat_results_Example_processed_file.ibd" name="ibd" compare="sim_size"/>
@@ -1069,7 +1064,7 @@
 - Peak binning: extracts peaks intensities, either peak height or area under curve (from a profile dataset) for a list of m/z (reference) values
 - m/z binning: generates new m/z bins
 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. 
-- ComBat batch correction: corrects the intensity values of picked m/z features according to batches given in an annotation table. For now, it can only be applied to m/z features after peak picking (=centroided data). The annotation table needs to contain the x and y coordinates for each pixel and a batch identifier (e.g. TMA_1, TMA_2, TMA_3). Additionally a condition column can be provided, which is only used for the PCA plots in the pdf file. Example of annotation file for ComBat batch correction:
+- ComBat batch correction: corrects the intensity values of picked m/z features according to batches given in an annotation table. For now, it can only be applied to m/z features after peak picking (=centroided data). The annotation table needs to contain the x and y coordinates for each pixel and a batch identifier (e.g. TMA_1, TMA_2, TMA_3). Additionally, a condition column can be provided, which is only used for the PCA plots in the pdf file. Example of annotation file for ComBat batch correction:
  
  ::