changeset 16:ed23ae226cdc draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6

--- a/msi_qualitycontrol.xml	Wed Aug 15 05:40:29 2018 -0400
+++ b/msi_qualitycontrol.xml	Wed Aug 22 13:43:49 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.6">
+<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.7">
     <description>
         mass spectrometry imaging QC
     </description>
@@ -48,16 +48,20 @@
 #elif $infile.ext == 'analyze75'
     msidata = readAnalyze('infile')
 #else
-    load('infile.RData')
+    loadRData <- function(fileName){
+    load(fileName)
+    get(ls()[ls() != "fileName"])
+    }
+    msidata = loadRData('infile.RData')
 #end if
 
-## create full matrix to make processed imzML files compatible with segmentation and other steps
-iData(msidata) <- iData(msidata)[]
-
 ## remove duplicated coordinates
 print(paste0(sum(duplicated(coord(msidata))), " duplicated coordinates were removed"))
 msidata <- msidata[,!duplicated(coord(msidata))]
 
+## create full matrix to make processed imzML files compatible with segmentation and other steps
+iData(msidata) <- iData(msidata)[]
+
 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)
 
 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
@@ -288,10 +292,6 @@
 
         colnames(position_df)[3] = "annotation"
 
-print(position_df)
-print(class(position_df\$x))
-print(class(position_df\$annotation))
-
         combine_plot = ggplot(position_df, aes(x=x, y=y, fill=annotation))+
                geom_tile() +
                coord_fixed()+
@@ -301,7 +301,7 @@
                theme(text=element_text(family="ArialMT", face="bold", size=12))+
                theme(legend.position="bottom",legend.direction="vertical")+
                theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
-               guides(fill=guide_legend(ncol=5,byrow=TRUE))
+               guides(fill=guide_legend(ncol=4,byrow=TRUE))
 
         print(combine_plot)
 
@@ -1083,13 +1083,15 @@
 
 This tool uses Cardinal to read files and create a quality control report with descriptive plots for mass spectrometry imaging data. 
 
-Input data: 3 types of input data can be used:
+Input data: 3 types of MSI data can be used:
 
 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
+- Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before the tools analysis starts. 
 - optional: tabular file with pixel annotations: x and y values in separate columns and the corresponding annotation in a third column
 
+
 Options: 
 
 - internal calibrants are used for m/z heatmaps (x-y grid), heatmap of number of calibrants per spectrum (x-y grid), zoomed in mass spectra, m/z accuracy