diff msi_preprocessing.xml @ 6:d3fd539f477e draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92

--- a/msi_preprocessing.xml	Tue Jun 19 18:08:01 2018 -0400
+++ b/msi_preprocessing.xml	Thu Jun 21 16:45:55 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.2">
+<tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.3">
     <description>
         mass spectrometry imaging preprocessing
     </description>
@@ -6,7 +6,6 @@
         <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
         <requirement type="package" version="2.2.1">r-gridextra</requirement>
         <requirement type="package" version="0.20-35">r-lattice</requirement>
-        <!--requirement type="package" version="3.34.9">bioconductor-limma</requirement-->
     </requirements>
     <command detect_errors="exit_code">
     <![CDATA[
@@ -34,10 +33,13 @@
 library(Cardinal)
 library(gridExtra)
 library(lattice)
-###library(limma)
 
 #if $infile.ext == 'imzml'
-    msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units")
+    #if str($processed_cond.processed_file) == "processed":
+        msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
+    #else
+        msidata <- readImzML('infile')
+    #end if
 #elif $infile.ext == 'analyze75'
     msidata = readAnalyze('infile')
 #else
@@ -417,11 +419,20 @@
         <param name="infile" type="data" format="imzml,rdata,danalyze75"
             label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData"
             help="load imzml and ibd file by uploading composite datatype imzml"/>
-        <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
-        <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm">
-            <option value="mz" >mz</option>
-            <option value="ppm" selected="True" >ppm</option>
-        </param>
+        <conditional name="processed_cond">
+            <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
+                <option value="no_processed" selected="True">not a processed imzML</option>
+                <option value="processed">processed imzML</option>
+            </param>
+            <when value="no_processed"/>
+            <when value="processed">
+                <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
+                <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
+                    <option value="mz" >mz</option>
+                    <option value="ppm" selected="True" >ppm</option>
+                </param>
+            </when>
+        </conditional>
         <repeat name="methods" title="Preprocessing" min="1" max="50">
             <conditional name="methods_conditional">
                 <param name="preprocessing_method" type="select" label="Select the preprocessing methods you want to apply">
@@ -501,7 +512,7 @@
                             <param name="units_diffalignment" type="select" display = "radio" optional = "False"
                                    label="units">
                                     <option value="ppm" selected="True">ppm</option>
-                                    <option value="Da">Da</option>
+                                    <option value="Da">m/z</option>
                             </param>
                         </when>
                         <when value="DP">
@@ -790,6 +801,7 @@
 - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value
 - Peak filtering: works only on centroided data (after peak picking and alignment or data reduction with peak filtering), removes peaks that occur only in a small proportion of pixels. If not sure which cutoff to chose run qualitycontrol first and decide according to the zero value plot.
 - Data reduction: binning, resampling or peak filtering to reduce data
+- Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. 
 
 
 Output: