diff mz_images.xml @ 9:08ebd8da780c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"

--- a/mz_images.xml	Wed May 13 14:27:51 2020 -0400
+++ b/mz_images.xml	Thu Sep 24 11:35:54 2020 +0000
@@ -64,7 +64,8 @@
         for (mass in 1:length(inputmz)){
 
                 print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", 
-                smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy)))}
+                smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy)))
+                title(inputnames[mass], adj = 0.5, line = 1)}
 
 
         ## optional svg output with original coordinates
@@ -99,7 +100,7 @@
 
              legend("$overlay_cond.legend_position",
                        fill=colourvector,
-                      legend=as.numeric(sort(as.character(inputmz))))
+                      legend=as.numeric(inputmz))
         #end if
 
     } else {print("The input m/z were invalid")}
@@ -134,7 +135,6 @@
             <option value="plasma">plasma</option>
             <option value="inferno">inferno</option>
         </param>
-        <param name="strip" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/>
         <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
         <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/>
         <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
@@ -182,7 +182,6 @@
             <param name="plusminus_dalton" value="0.25"/>
             <param name="filename" value="Testfile_imzml"/>
             <param name="image_contrast" value="histogram"/>
-            <param name="strip" value="True"/>
             <param name="colorkey" value="True"/>
             <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/>
         </test>
@@ -195,7 +194,6 @@
             <param name="filename" value="Testfile_analyze75"/>
             <param name="colorscale" value="magma"/>
             <param name="image_smoothing" value="gaussian"/>
-            <param name="strip" value="False"/>
             <param name="colorkey" value="True"/>
             <param name="svg_pixelimage" value="True"/>
             <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>
@@ -207,7 +205,6 @@
             <param name="mz_column" value="1"/>
             <param name="name_column" value="2"/>
             <param name="plusminus_dalton" value="0.5"/>
-            <param name="strip" value="True"/>
             <param name="colorkey" value="True"/>
             <param name="filename" value="Testfile_rdata"/>
             <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/>
@@ -219,7 +216,6 @@
             <param name="name_column" value="1"/>
             <param name="plusminus_dalton" value="0.5"/>
             <param name="colorscale" value="plasma"/>
-            <param name="strip" value="True"/>
             <param name="colorkey" value="False"/>
             <param name="filename" value="Testfile_rdata"/>
             <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/>
@@ -228,7 +224,7 @@
             <expand macro="processed_infile_imzml"/>
             <conditional name="processed_cond">
                 <param name="processed_file" value="processed"/>
-                <param name="accuracy" value="100"/>
+                <param name="accuracy" value="200"/>
                 <param name="units" value="ppm"/>
             </conditional>
             <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>