Mercurial > repos > galaxyp > cardinal_segmentations

changeset 1:98d48f081ad9 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
author galaxyp
date Thu, 25 Oct 2018 07:25:52 -0400
parents e56a955cd1c0
children 034885df9b09
files macros.xml segmentation.xml test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_rdata.pdf test-data/Plot_analyze75.pdf test-data/Plot_analyze75_allpixels.pdf test-data/Plot_empty_spectra.pdf test-data/Plot_imzml.pdf test-data/Plot_rdata.pdf test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/analyze75.svg test-data/analyze75_filtered2.pdf test-data/analyze_filteredoutside.RData test-data/centroids_rdata.pdf test-data/cluster_skm.RData test-data/imzml_filtered2.RData test-data/imzml_filtered2.pdf test-data/imzml_filtered3.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.RData test-data/imzml_filtered4.pdf test-data/imzml_filtered5.RData test-data/imzml_filtered5.pdf test-data/kmeans_analyze.pdf test-data/pca_imzml.pdf test-data/rdata_notfiltered.RData test-data/rdata_notfiltered.pdf test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata
diffstat 42 files changed, 51 insertions(+), 36 deletions(-) [+]
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line diff
--- a/macros.xml	Mon Oct 01 01:05:00 2018 -0400
+++ b/macros.xml	Thu Oct 25 07:25:52 2018 -0400
@@ -4,10 +4,17 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
+            <requirement type="package" version="3.5.1">r-base</requirement>
             <yield/>
         </requirements>
     </xml>
 
+    <xml name="print_version">
+        <version_command><![CDATA[
+echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+        ]]></version_command>
+    </xml>
+
     <token name="@INPUT_LINKING@"><![CDATA[
         #if $infile.ext == 'imzml'
             ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
@@ -33,14 +40,14 @@
 
         #if $infile.ext == 'imzml'
             #if str($processed_cond.processed_file) == "processed":
-                msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
+                msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE)
                 centroided(msidata) = $centroids
             #else
-                msidata <- readImzML('infile')
+                msidata <- readImzML('infile', attach.only=TRUE)
                 centroided(msidata) = $centroids
             #end if
         #elif $infile.ext == 'analyze75'
-            msidata = readAnalyze('infile')
+            msidata = readAnalyze('infile', attach.only=TRUE)
             centroided(msidata) = $centroids
         #else
             msidata = loadRData('infile.RData')
@@ -177,7 +184,8 @@
         <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name">
             <sanitizer invalid_char="">
                 <valid initial="string.ascii_letters,string.digits">
-                    <add value="_" />
+                    <add value="_"/>
+                    <add value=" "/>
                 </valid>
             </sanitizer>
         </param>
@@ -198,12 +206,12 @@
         <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
     </xml>
 
-    <xml name="reading_2_column_mz_tabular">
-        <param name="calibrant_file" type="data" optional="true" format="tabular"
+    <xml name="reading_2_column_mz_tabular" token_optional="false">
+        <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular"
             label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/>
-        <param name="mz_column" data_ref="calibrant_file" label="Column with m/z values" type="data_column"/>
-        <param name="name_column" data_ref="calibrant_file" label="Column with name of m/z values" type="data_column"/>
-        <param name="calibrant_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
+        <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/>
+        <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/>
+        <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>
     </xml>
 
     <xml name="reading_pixel_annotations">
--- a/segmentation.xml	Mon Oct 01 01:05:00 2018 -0400
+++ b/segmentation.xml	Thu Oct 25 07:25:52 2018 -0400
@@ -1,11 +1,11 @@
-<tool id="cardinal_segmentations" name="MSI segmentation" version="@VERSION@.0">
+<tool id="cardinal_segmentations" name="MSI segmentation" version="@VERSION@.1">
     <description>mass spectrometry imaging spatial clustering</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.2.1">r-gridextra</requirement>
-        <requirement type="package" version="0.20-35">r-lattice</requirement>
+        <requirement type="package" version="2.3">r-gridextra</requirement>
+        <requirement type="package" version="0.20_35">r-lattice</requirement>
     </expand>
     <command detect_errors="exit_code">
     <![CDATA[
@@ -78,7 +78,7 @@
         #if str( $segm_cond.segmentationtool ) == 'pca':
             print('pca')
             ##pca
-            
+
             component_vector = character()
             for (numberofcomponents in 1:$segm_cond.pca_ncomp)
             {component_vector[numberofcomponents]= paste0("PC", numberofcomponents)}
@@ -101,10 +101,13 @@
             pcascores = (pca_result@resultData\$ncomp\$scores) ### scores for each pixel
 
             ## pixel names and coordinates
-            pixel_names = gsub(", y = ", "_", rownames(pcascores))
-            pixel_names = gsub(" = ", "y_", pixel_names)
-            x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
-            y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
+            ## to remove potential sample names and z dimension, split at comma and take only x and y 
+            x_coords = unlist(lapply(strsplit(rownames(pcascores), ","), `[[`, 1))
+            y_coords = unlist(lapply(strsplit(rownames(pcascores), ","), `[[`, 2))
+            x_coordinates = gsub("x = ","",x_coords)
+            y_coordinates = gsub(" y = ","",y_coords)
+
+            pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
             pcascores2 = data.frame(pixel_names, x_coordinates, y_coordinates, pcascores)
             colnames(pcascores2) = c("pixel names", "x", "y", colnames(pcascores))
             write.table(pcaloadings2, file="$mzfeatures", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
@@ -132,10 +135,12 @@
             skm_clusters = cbind(skm_clusters, skm_cluster) }
 
             ## pixel names and coordinates
-            pixel_names = gsub(", y = ", "_", rownames(skm_clusters))
-            pixel_names = gsub(" = ", "y_", pixel_names)
-            x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
-            y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
+            ## to remove potential sample names and z dimension, split at comma and take only x and y 
+            x_coords = unlist(lapply(strsplit(rownames(skm_clusters), ","), `[[`, 1))
+            y_coords = unlist(lapply(strsplit(rownames(skm_clusters), ","), `[[`, 2))
+            x_coordinates = gsub("x = ","",x_coords)
+            y_coordinates = gsub(" y = ","",y_coords)
+            pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
             skm_clusters2 = data.frame(pixel_names, x_coordinates, y_coordinates, skm_clusters)
             colnames(skm_clusters2) = c("pixel names", "x", "y",names(skm@resultData))
 
@@ -168,10 +173,12 @@
             ssc_classes = cbind(ssc_classes, ssc_class) }
 
             ## pixel names and coordinates
-            pixel_names = gsub(", y = ", "_", rownames(ssc_classes))
-            pixel_names = gsub(" = ", "y_", pixel_names)
-            x_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,2]
-            y_coordinates = matrix(unlist(strsplit(pixel_names, "_")), ncol=3, byrow=TRUE)[,3]
+            ## to remove potential sample names and z dimension, split at comma and take only x and y 
+            x_coords = unlist(lapply(strsplit(rownames(ssc_classes), ","), `[[`, 1))
+            y_coords = unlist(lapply(strsplit(rownames(ssc_classes), ","), `[[`, 2))
+            x_coordinates = gsub("x = ","",x_coords)
+            y_coordinates = gsub(" y = ","",y_coords)
+            pixel_names = paste0("xy_", x_coordinates, "_", y_coordinates)
             ssc_classes2 = data.frame(pixel_names, x_coordinates, y_coordinates, ssc_classes)
             colnames(ssc_classes2) = c("pixel names", "x", "y", names(ssc@resultData))
 
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--- a/test-data/analyze75.svg	Mon Oct 01 01:05:00 2018 -0400
+++ b/test-data/analyze75.svg	Thu Oct 25 07:25:52 2018 -0400
@@ -1,15 +1,15 @@
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-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="216pt" height="216pt" viewBox="0 0 216 216" version="1.1">
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="504pt" height="504pt" viewBox="0 0 504 504" version="1.1">
 <g id="surface1">
-<rect x="0" y="0" width="216" height="216" style="fill:rgb(100%,100%,100%);fill-opacity:1;stroke:none;"/>
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-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0%,0%);fill-opacity:1;" d="M 72 0 L 144 0 L 144 72 L 72 72 Z M 72 0 "/>
-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0.392157%,33.333333%);fill-opacity:1;" d="M 72 72 L 144 72 L 144 144 L 72 144 Z M 72 72 "/>
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-<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.960784%,100%);fill-opacity:1;" d="M 144 144 L 216 144 L 216 216 L 144 216 Z M 144 144 "/>
+<rect x="0" y="0" width="504" height="504" style="fill:rgb(100%,100%,100%);fill-opacity:1;stroke:none;"/>
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+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.568627%,81.568627%);fill-opacity:1;" d="M 336 336 L 504 336 L 504 168 L 336 168 Z M 336 336 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.960784%,100%);fill-opacity:1;" d="M 336 168 L 504 168 L 504 0 L 336 0 Z M 336 168 "/>
 </g>
 </svg>
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