diff spectra_plots.xml @ 9:006fc980af63 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"

--- a/spectra_plots.xml	Wed May 13 17:57:37 2020 +0000
+++ b/spectra_plots.xml	Tue Nov 03 22:35:49 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.0">
+<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.1">
     <description>
         mass spectrometry imaging mass spectra plots
     </description>
@@ -6,9 +6,9 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.2.1">r-ggplot2</requirement>
+        <requirement type="package" version="3.3.2">r-ggplot2</requirement>
         <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="1.0.0">r-scales</requirement>
+        <requirement type="package" version="1.1.1">r-scales</requirement>
     </expand>
     <command detect_errors="exit_code">
     <![CDATA[
@@ -82,7 +82,7 @@
                 merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"), all.x=TRUE)
                 merged_annotation[is.na(merged_annotation)] = "NA"
                 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
-                msidata\$annotation = as.factor(merged_annotation[,4])
+                msidata\$annotation = factor(merged_annotation[,4], levels = unique(as.character(merged_annotation[,4]))) ## keep the right order
 
                     ## overview plot over annotated samples
                     number_combined = length(levels(msidata\$annotation))
@@ -214,7 +214,7 @@
 
                     #if $fullmz:
                     ## plot full mz for single tabular mz
-                        print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable))
+                        print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable, col="black"))
                     #end if
 
                     pixelname = paste0("x = ", x_coord,", ", "y = ", y_coord)
@@ -261,7 +261,7 @@
                 }
 
                     ## print single tabular mz; manual zoom
-                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax)))
+                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black"))
 
                 #end for
 
@@ -306,7 +306,7 @@
                             }
 
                                 ## print single tabular mz; tabular zoom
-                                print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax)))
+                                print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax), col="black"))
                             }
                         }
 
@@ -329,7 +329,7 @@
 
                     #if $fullmz:
 
-                        print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable))
+                        print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable, col="black"))
                     #end if
 
         ##################### II) Sample: plot zoom-in mass spectrum ##########
@@ -366,7 +366,7 @@
                         }
                 }
 
-                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax)))
+                    print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black"))
 
             #end for
 
@@ -401,7 +401,7 @@
                                     }
                                 )   
 
-                        print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax)))
+                        print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax), col="black"))
                 }
             }
 
@@ -456,7 +456,7 @@
         <expand macro="reading_msidata"/>
         <expand macro="pdf_filename"/>
         <conditional name="pixel_conditional">
-            <param name="pixel_type" type="select" label="Choose spectra (pixel)">
+            <param name="pixel_type" type="select" label="Choose spectra (pixel) and/or add spectra annotations">
                 <option value="all_pixel" selected="True" >All spectra</option>
                 <option value="tabular_pixel">Single spectra</option>
             </param>
@@ -588,7 +588,7 @@
             <expand macro="processed_infile_imzml"/>
             <conditional name="processed_cond">
                 <param name="processed_file" value="processed"/>
-                <param name="accuracy" value="50"/>
+                <param name="accuracy" value="100"/>
                 <param name="units" value="ppm"/>
             </conditional>
             <conditional name="pixel_conditional">