--- a/preprocessing.xml	Thu Sep 24 11:43:31 2020 +0000
+++ b/preprocessing.xml	Sun Sep 27 11:10:30 2020 +0000
@@ -74,7 +74,7 @@
     ## Choose random spectra for QC plots
     random_spectra = sample(pixels(msidata), 4, replace=FALSE)
     par(oma=c(0,0,2,0))
-    print(plot(msidata, pixel=random_spectra))
+    print(plot(msidata, pixel=random_spectra, col="black"))
     title("Input spectra", outer=TRUE, line=0)
 
     ############################### Preprocessing steps ###########################
@@ -88,10 +88,6 @@
             print('Normalization')
             ##normalization
 
-            if (class(msidata) == "MSProcessedImagingExperiment"){
-                msidata = as(msidata, "MSContinuousImagingExperiment")
-            }
-
             msidata = normalize(msidata, method="$method.methods_conditional.methods_for_normalization.normalization_method")
             msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
 
@@ -105,7 +101,7 @@
             normalized = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, normalized)
             vectorofactions = append(vectorofactions, "normalized")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after normalization", outer=TRUE, line=0)
 
     ############################### Baseline reduction ###########################
@@ -114,10 +110,6 @@
             print('Baseline_reduction')
             ##baseline reduction
 
-            if (class(msidata) == "MSProcessedImagingExperiment"){
-                msidata = as(msidata, "MSContinuousImagingExperiment")
-            }
-
             msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline, spar=$method.methods_conditional.spar_baseline)
             msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
 
@@ -130,7 +122,7 @@
             baseline = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, baseline)
             vectorofactions = append(vectorofactions, "baseline red.")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after baseline reduction", outer=TRUE, line=0)
 
     ############################### Smoothing ###########################
@@ -139,11 +131,6 @@
             print('Smoothing')
             ## Smoothing
 
-            if (class(msidata) == "MSProcessedImagingExperiment"){
-                msidata = as(msidata, "MSContinuousImagingExperiment")
-            }
-
-
             #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
                 print('gaussian smoothing')
 
@@ -176,7 +163,7 @@
             smoothed = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, smoothed)
             vectorofactions = append(vectorofactions, "smoothed")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after smoothing", outer=TRUE, line=0)
 
 
@@ -211,7 +198,7 @@
             mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, mz_aligned)
             vectorofactions = append(vectorofactions, "mz aligned")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after m/z alignment", outer=TRUE, line=0)
 
 
@@ -240,10 +227,6 @@
             #end if
             msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
 
-            #if str($method.methods_conditional.imzml_output) == "cont_format":
-                #set $continuous_format = True
-            #end if
-
 
             ############################### QC ###########################
 
@@ -254,7 +237,7 @@
             picked = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, picked)
             vectorofactions = append(vectorofactions, "picked")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after peak picking", outer=TRUE, line=0)
 
     ############################### Peak alignment ###########################
@@ -285,9 +268,6 @@
 
             msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
 
-            #if str($method.methods_conditional.imzml_output) == "cont_format":
-                #set $continuous_format = True
-            #end if
 
             ############################### QC ###########################
 
@@ -298,7 +278,7 @@
             aligned = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, aligned)
             vectorofactions = append(vectorofactions, "aligned")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after alignment", outer=TRUE, line=0)
 
     ############################### Peak filtering ###########################
@@ -318,7 +298,7 @@
             filtered = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, filtered)
             vectorofactions = append(vectorofactions, "filtered")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after filtering", outer=TRUE, line=0)
 
     ############################### Peak binning ###########################
@@ -343,7 +323,7 @@
             peak_binned = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, peak_binned)
             vectorofactions = append(vectorofactions, "peak binned")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after peak binning", outer=TRUE, line=0)
 
 
@@ -387,7 +367,7 @@
             reduced = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, reduced)
             vectorofactions = append(vectorofactions, "reduced")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after m/z binning", outer=TRUE, line=0)
 
         ############################### Transformation ###########################
@@ -430,7 +410,7 @@
             transformed = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, transformed)
             vectorofactions = append(vectorofactions, "transformed")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after transformation", outer=TRUE, line=0)
 
             #end if
@@ -440,6 +420,10 @@
     ################################################################################
 
     ## save msidata as imzML file, will only work if there is at least 1 m/z left
+    
+    #if str($imzml_output) == "cont_format":
+        #set $continuous_format = True
+    #end if
 
         if (nrow(msidata) > 0){
             ## make sure that coordinates are integers
@@ -578,7 +562,6 @@
                         <when value="mad"/>
                         <when value="simple"/>
                     </conditional>
-                <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/>
                 </when>
                 <when value="Peak_alignment">
                     <param name="value_diffalignment" type="float" value="200"
@@ -597,7 +580,6 @@
                             <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/>
                         </when>
                     </conditional>
-                <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format" help= "Processed imzML works only in MALDIquant tools, not yet in MSI tools (Cardinal)"/>
                 </when>
                 <when value="Peak_filtering">
                     <param name="frequ_filtering" type="float" value="0.01" max="1" min="0" label="Minimum frequency" help="Peaks that occur in the dataset in lesser proportion than this will be dropped (0.01 --> filtering for 1% of spectra)"/>
@@ -661,6 +643,7 @@
                 </when>
             </conditional>
         </repeat>
+        <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/>
     </inputs>
     <outputs>
         <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
@@ -696,13 +679,11 @@
                     <param name="blocks_picking" value="3"/>
                     <param name="window_picking" value="3"/>
                     <param name="SNR_picking_method" value="3"/>
-                    <param name="imzml_output" value="cont_format"/>
                 </conditional>
             </repeat>
             <repeat name="methods">
                 <conditional name="methods_conditional">
                     <param name="preprocessing_method" value="Peak_alignment"/>
-                    <param name="imzml_output" value="cont_format"/>
                 </conditional>
             </repeat>
             <repeat name="methods">
@@ -719,6 +700,7 @@
                         </conditional>
                 </conditional>
             </repeat>
+            <param name="imzml_output" value="cont_format"/>
             <output name="QC_overview" file="preprocessing_results1.pdf" compare="sim_size"/>
             <output name="outfile_imzml" ftype="imzml" file="preprocessing_results1.imzml.txt" compare="sim_size">
                 <extra_files type="file" file="preprocessing_results1.imzml" name="imzml" lines_diff="6"/>
@@ -736,15 +718,14 @@
                     <conditional name="methods_for_picking">
                         <param name="picking_method" value="adaptive"/>
                     </conditional>
-                    <param name="imzml_output" value="cont_format"/>
                 </conditional>
             </repeat>
             <repeat name="methods">
                 <conditional name="methods_conditional">
                     <param name="preprocessing_method" value="Peak_alignment"/>
-                    <param name="imzml_output" value="cont_format"/>
                 </conditional>
             </repeat>
+            <param name="imzml_output" value="cont_format"/>
             <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/>
             <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size">
                 <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/>