changeset 3:f172efe92629 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
author galaxyp
date Thu, 28 Feb 2019 09:27:06 -0500
parents 1b875f0b8024
children 141a9288be9c
files preprocessing.xml test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results2.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results3.pdf test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.pdf test-data/preprocessing_results5.RData test-data/preprocessing_results5.pdf
diffstat 19 files changed, 56 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/preprocessing.xml	Fri Feb 15 10:22:14 2019 -0500
+++ b/preprocessing.xml	Thu Feb 28 09:27:06 2019 -0500
@@ -60,7 +60,13 @@
     maxmz = round(max(mz(msidata)), digits=2)
     QC_numbers= data.frame(inputdata = c(minmz, maxmz,maxfeatures, pixelcount))
     vectorofactions = "inputdata"
-    plot(msidata, pixel = 1:pixelcount, main="Average spectrum of input file")
+    ## Choose random spectra for QC plots
+    random_spectra = sample(pixels(msidata), 4, replace=FALSE)
+    par(mfrow = c(2, 2), oma=c(0,0,2,0))
+    for (random_sample in 1:length(random_spectra)){
+        plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))}
+    title("Input spectra", outer=TRUE, line=0)
+
 
     ############################### Preprocessing steps ###########################
     ###############################################################################
@@ -84,7 +90,10 @@
             normalized = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, normalized)
             vectorofactions = append(vectorofactions, "normalized")
-            plot(msidata, pixel = 1:pixelcount, main="Average spectrum after normalization")
+            par(mfrow = c(2, 2), oma=c(0,0,2,0))
+            for (random_sample in 1:length(random_spectra)){
+                plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))}
+            title("Spectra after normalization", outer=TRUE, line=0)
 
     ############################### Baseline reduction ###########################
 
@@ -103,7 +112,9 @@
             baseline = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, baseline)
             vectorofactions = append(vectorofactions, "baseline red.")
-            plot(msidata, pixel = 1:pixelcount, main="Average spectrum after baseline reduction")
+            for (random_sample in 1:length(random_spectra)){
+                plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))}
+            title("Spectra after baseline reduction", outer=TRUE, line=0)
 
     ############################### Smoothing ###########################
 
@@ -136,7 +147,9 @@
             smoothed = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, smoothed)
             vectorofactions = append(vectorofactions, "smoothed")
-            plot(msidata, pixel = 1:pixelcount, main="Average spectrum after smoothing")
+            for (random_sample in 1:length(random_spectra)){
+                plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))}
+            title("Spectra after smoothing", outer=TRUE, line=0)
 
     ############################### Peak picking ###########################
 
@@ -170,7 +183,9 @@
             picked = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, picked)
             vectorofactions = append(vectorofactions, "picked")
-            plot(msidata, pixel = 1:pixelcount, main="Average spectrum after peak picking")
+            for (random_sample in 1:length(random_spectra)){
+                plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))}
+            title("Spectra after peak picking", outer=TRUE, line=0)
 
     ############################### Peak alignment ###########################
 
@@ -184,8 +199,8 @@
 
             #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_table':
 
-                align_reference_table = read.delim("$method.methods_conditional.align_ref_type.mz_tabular", header = $method.methods_conditional.align_ref_type.align_mass_header, stringsAsFactors = FALSE)
-                align_reference_column = align_reference_table[,$method.methods_conditional.align_ref_type.align_mass_column]
+                align_reference_table = read.delim("$method.methods_conditional.align_ref_type.mz_tabular", header = $method.methods_conditional.align_ref_type.feature_header, stringsAsFactors = FALSE)
+                align_reference_column = align_reference_table[,$method.methods_conditional.align_ref_type.feature_column]
                 align_peak_reference = align_reference_column[align_reference_column>=min(mz(msidata)) & align_reference_column<=max(mz(msidata))]
                 if (length(align_peak_reference) == 0)
                     {align_peak_reference = 0}
@@ -217,7 +232,9 @@
             aligned = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, aligned)
             vectorofactions = append(vectorofactions, "aligned")
-            plot(msidata, pixel = 1:pixelcount, main="Average spectrum after alignment")
+            for (random_sample in 1:length(random_spectra)){
+                plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))}
+            title("Spectra after alignment", outer=TRUE, line=0)
 
     ############################### Peak filtering ###########################
 
@@ -235,7 +252,9 @@
             filtered = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, filtered)
             vectorofactions = append(vectorofactions, "filtered")
-            plot(msidata, pixel = 1:pixelcount, main="Average spectrum after filtering")
+            for (random_sample in 1:length(random_spectra)){
+                plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))}
+            title("Spectra after filtering", outer=TRUE, line=0)
 
     ############################### Data reduction ###########################
 
@@ -266,8 +285,8 @@
 
                 #if str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'table':
 
-                    reference_table = read.delim("$method.methods_conditional.methods_for_reduction.ref_type.mz_tabular", header = $method.methods_conditional.methods_for_reduction.ref_type.mass_header, stringsAsFactors = FALSE)
-                    reference_column = reference_table[,$method.methods_conditional.methods_for_reduction.ref_type.mass_column]
+                    reference_table = read.delim("$method.methods_conditional.methods_for_reduction.ref_type.mz_tabular", header = $method.methods_conditional.methods_for_reduction.ref_type.feature_header, stringsAsFactors = FALSE)
+                    reference_column = reference_table[,$method.methods_conditional.methods_for_reduction.ref_type.feature_column]
                     peak_reference = reference_column[reference_column>min(mz(msidata)) & reference_column<max(mz(msidata))]
 
                 #elif str( $method.methods_conditional.methods_for_reduction.ref_type.reference_datatype) == 'msidata_ref':
@@ -287,7 +306,9 @@
             reduced = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, reduced)
             vectorofactions = append(vectorofactions, "reduced")
-            plot(msidata, pixel = 1:pixelcount, main="Average spectrum after data reduction")
+            for (random_sample in 1:length(random_spectra)){
+                plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))}
+            title("Spectra after data reduction", outer=TRUE, line=0)
 
         ############################### Transformation ###########################
 
@@ -328,7 +349,9 @@
             transformed = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, transformed)
             vectorofactions = append(vectorofactions, "transformed")
-            plot(msidata, pixel = 1:pixelcount, main="Average spectrum after transformation")
+            for (random_sample in 1:length(random_spectra)){
+                plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))}
+            title("Spectra after transformation", outer=TRUE, line=0)
 
             #end if
     #end for
@@ -340,6 +363,9 @@
 
     #if str($imzml_output) == "imzml_format":
         if (nrow(msidata) > 0){
+            ## make sure that coordinates are integers
+            coord(msidata)\$y = as.integer(coord(msidata)\$y)
+            coord(msidata)\$x = as.integer(coord(msidata)\$x)
             writeImzML(msidata, "out")}
     #elif str($imzml_output) == "rdata_format":
         ## save as (.RData)
@@ -443,7 +469,7 @@
                                    label="diff.max" help="Peaks that differ less than this value will be aligned together"/>
                             <param name="units_diffalignment" type="select" display="radio" optional="False" label="units">
                                     <option value="ppm" selected="True">ppm</option>
-                                    <option value="Da">m/z</option>
+                                    <option value="mz">m/z</option>
                             </param>
                         </when>
                         <when value="DP">
Binary file test-data/preprocessing_results1.ibd has changed
--- a/test-data/preprocessing_results1.imzml	Fri Feb 15 10:22:14 2019 -0500
+++ b/test-data/preprocessing_results1.imzml	Thu Feb 28 09:27:06 2019 -0500
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{002DF5BA-0549-44DF-A8BB-27DA3E197EB7}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0379019A6F9D0B55F9217420030633F7163AF9D3" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{728FBFFE-E6FC-4283-8068-393A66F6BD5C}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="375094460F3B80674CB2F541DCD9928B3D61B2FF" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/preprocessing_results1.imzml.txt	Fri Feb 15 10:22:14 2019 -0500
+++ b/test-data/preprocessing_results1.imzml.txt	Thu Feb 28 09:27:06 2019 -0500
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-r--r-- 1 meli meli    96 Feb 12 21:24 ibd
--rw-r--r-- 1 meli meli 16714 Feb 12 21:24 imzml
+-rw-r--r-- 1 meli meli    96 Feb 24 14:11 ibd
+-rw-r--r-- 1 meli meli 16714 Feb 24 14:11 imzml
Binary file test-data/preprocessing_results1.pdf has changed
Binary file test-data/preprocessing_results2.ibd has changed
--- a/test-data/preprocessing_results2.imzml	Fri Feb 15 10:22:14 2019 -0500
+++ b/test-data/preprocessing_results2.imzml	Thu Feb 28 09:27:06 2019 -0500
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{84BEACDD-B841-4730-81A0-A19A28C7B48A}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1BC49DCCC566E7A6938CE3DE62090650C2A04798" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{40F230A1-1893-4A8C-BAE2-A8BBEF24DB20}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="417ADF38FBC4D0304A9B75B4C85799137846DD2F" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/preprocessing_results2.imzml.txt	Fri Feb 15 10:22:14 2019 -0500
+++ b/test-data/preprocessing_results2.imzml.txt	Thu Feb 28 09:27:06 2019 -0500
@@ -1,4 +1,4 @@
 imzML file:
 total 80
--rw-r--r-- 1 meli meli 54720 Feb 12 21:25 ibd
--rw-r--r-- 1 meli meli 21132 Feb 12 21:25 imzml
+-rw-r--r-- 1 meli meli 54720 Feb 24 14:12 ibd
+-rw-r--r-- 1 meli meli 21132 Feb 24 14:12 imzml
Binary file test-data/preprocessing_results2.pdf has changed
Binary file test-data/preprocessing_results3.ibd has changed
--- a/test-data/preprocessing_results3.imzml	Fri Feb 15 10:22:14 2019 -0500
+++ b/test-data/preprocessing_results3.imzml	Thu Feb 28 09:27:06 2019 -0500
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{4C387879-DE12-49A4-878F-6980D6F7C6F0}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="94ED775BCF16644D23DACFCA1E62D28D5C755178" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{D767424F-5E74-45AB-AF1B-0D25244B435B}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="445E32981D0B3D08ED2BA74E11500A3A08CDB9B7" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/preprocessing_results3.imzml.txt	Fri Feb 15 10:22:14 2019 -0500
+++ b/test-data/preprocessing_results3.imzml.txt	Thu Feb 28 09:27:06 2019 -0500
@@ -1,4 +1,4 @@
 imzML file:
 total 36
--rw-r--r-- 1 meli meli 14216 Feb 12 21:26 ibd
--rw-r--r-- 1 meli meli 16824 Feb 12 21:26 imzml
+-rw-r--r-- 1 meli meli 14216 Feb 24 14:12 ibd
+-rw-r--r-- 1 meli meli 16824 Feb 24 14:12 imzml
Binary file test-data/preprocessing_results3.pdf has changed
Binary file test-data/preprocessing_results4.ibd has changed
--- a/test-data/preprocessing_results4.imzml	Fri Feb 15 10:22:14 2019 -0500
+++ b/test-data/preprocessing_results4.imzml	Thu Feb 28 09:27:06 2019 -0500
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{26018306-9D72-49F5-89CB-68E4DDE0527C}" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="BA6411EC5A5A59ABE5BD7005F4ED8FCEBA775A8E" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{FE932E04-42E4-4D89-B721-2A6CE83250B6}" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="36C7C916C176DD85CBBF4B7FA969C92B9403768D" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/preprocessing_results4.imzml.txt	Fri Feb 15 10:22:14 2019 -0500
+++ b/test-data/preprocessing_results4.imzml.txt	Thu Feb 28 09:27:06 2019 -0500
@@ -1,4 +1,4 @@
 imzML file:
 total 28
--rw-r--r-- 1 meli meli  6376 Feb 12 21:29 ibd
--rw-r--r-- 1 meli meli 16801 Feb 12 21:29 imzml
+-rw-r--r-- 1 meli meli  6376 Feb 24 14:13 ibd
+-rw-r--r-- 1 meli meli 16801 Feb 24 14:13 imzml
Binary file test-data/preprocessing_results4.pdf has changed
Binary file test-data/preprocessing_results5.RData has changed
Binary file test-data/preprocessing_results5.pdf has changed