Mercurial > repos > galaxyp > cardinal_preprocessing

changeset 11:e86a8be551b9 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0c667acd7cc0d0ef6c4e979ca29372b8c0d92c23"
author galaxyp
date Tue, 06 Oct 2020 08:12:49 +0000
parents 5abc3ab4792c
children e0669b1854b1
files preprocessing.xml test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf 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.ibd test-data/preprocessing_results5.imzml test-data/preprocessing_results5.imzml.txt test-data/preprocessing_results5.pdf
diffstat 25 files changed, 29 insertions(+), 27 deletions(-) [+]
line wrap: on
line diff
--- a/preprocessing.xml	Sun Sep 27 11:10:30 2020 +0000
+++ b/preprocessing.xml	Tue Oct 06 08:12:49 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.0">
+<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1">
     <description>
         mass spectrometry imaging preprocessing
     </description>
@@ -336,10 +336,12 @@
 
                 #if str($processed_cond.processed_file) == "processed":
 
-                msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
+                msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
                 
                 #else 
-                    msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)
+                    ## continuous file cannot be binned from m/z to m/z, therefore first cut m/z range and then do mzbin:
+                    msidata = msidata[mz(msidata) >= $method.methods_conditional.mz_range.min_mz & mz(msidata) <= $method.methods_conditional.mz_range.max_mz,]
+                    msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun="$method.methods_conditional.bin_fun")
                 #end if
 
 		   
Binary file test-data/QC_analyze75.pdf has changed
Binary file test-data/QC_empty_spectra.pdf has changed
Binary file test-data/QC_imzml.pdf has changed
Binary file test-data/QC_rdata.pdf has changed
Binary file test-data/preprocessing_results1.ibd has changed
--- a/test-data/preprocessing_results1.imzml	Sun Sep 27 11:10:30 2020 +0000
+++ b/test-data/preprocessing_results1.imzml	Tue Oct 06 08:12:49 2020 +0000
@@ -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="25fb4349-d529-4b12-8523-a6aa0306ecf4" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7f41f9f5efcb31248caefc91b7d6edce87d7f42c" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="07177fdd-3760-4df6-8fe2-53d28b280ae8" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="749fe32c8243da06001cf4643c5ce4f1ef5a98a8" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/preprocessing_results1.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
+++ b/test-data/preprocessing_results1.imzml.txt	Tue Oct 06 08:12:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-r--r-- 1 meli meli   216 Mai 10 17:37 ibd
--rw-r--r-- 1 meli meli 18090 Mai 10 17:37 imzml
+-rw-rw-r-- 1 meli meli   216 Oct  5 19:57 ibd
+-rw-rw-r-- 1 meli meli 18090 Oct  5 19:57 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	Sun Sep 27 11:10:30 2020 +0000
+++ b/test-data/preprocessing_results2.imzml	Tue Oct 06 08:12:49 2020 +0000
@@ -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="fa59b434-12e0-47fe-b338-814c92daa7d6" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5764be27b51a23d8c23e4c93befb9d8e57161bd9" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="503079b4-538a-4be6-b70d-e52542c66482" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="a597fe6a0184ef339105b3a932f58726a9af549b" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/preprocessing_results2.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
+++ b/test-data/preprocessing_results2.imzml.txt	Tue Oct 06 08:12:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 64
--rw-r--r-- 1 meli meli 37404 Mai 10 17:38 ibd
--rw-r--r-- 1 meli meli 22796 Mai 10 17:38 imzml
+-rw-rw-r-- 1 meli meli 37404 Oct  5 19:57 ibd
+-rw-rw-r-- 1 meli meli 22796 Oct  5 19:57 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	Sun Sep 27 11:10:30 2020 +0000
+++ b/test-data/preprocessing_results3.imzml	Tue Oct 06 08:12:49 2020 +0000
@@ -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="d11b7693-3397-4d1f-9e67-29d952701100" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="94906879d47bbdcf97126d50c906dfd76e6681e4" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="be549a7e-87af-4413-9b4c-27221f55ee9a" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4ee7ca6fb3f60e1adbe196068f86bc3209bace58" />
 			<cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/preprocessing_results3.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
+++ b/test-data/preprocessing_results3.imzml.txt	Tue Oct 06 08:12:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-r--r-- 1 meli meli   960 Mai 10 17:39 ibd
--rw-r--r-- 1 meli meli 18112 Mai 10 17:39 imzml
+-rw-rw-r-- 1 meli meli   960 Oct  5 19:58 ibd
+-rw-rw-r-- 1 meli meli 18112 Oct  5 19:58 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	Sun Sep 27 11:10:30 2020 +0000
+++ b/test-data/preprocessing_results4.imzml	Tue Oct 06 08:12:49 2020 +0000
@@ -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="9a685278-3bf0-48b5-b7c7-73a7a92625b2" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="036c4b8bf3f2f5a42a223ffd0b895f08b0a65f36" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="48842eaf-40e5-4a3f-831c-2d7a3b7e04b9" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2010ba5b7d44695d891cfe3b6674a5699fa610c0" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/preprocessing_results4.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
+++ b/test-data/preprocessing_results4.imzml.txt	Tue Oct 06 08:12:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 84
--rw-rw-r-- 1 meli meli 62696 Sep 20 11:48 ibd
--rw-rw-r-- 1 meli meli 18199 Sep 20 11:48 imzml
+-rw-rw-r-- 1 meli meli 62696 Oct  5 19:58 ibd
+-rw-rw-r-- 1 meli meli 18199 Oct  5 19:58 imzml
Binary file test-data/preprocessing_results4.pdf has changed
Binary file test-data/preprocessing_results5.ibd has changed
--- a/test-data/preprocessing_results5.imzml	Sun Sep 27 11:10:30 2020 +0000
+++ b/test-data/preprocessing_results5.imzml	Tue Oct 06 08:12:49 2020 +0000
@@ -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="3aff713c-00ec-422d-b63d-efd45fbdd7cc" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9316138c1e7484662943bb206c79c2d074121530" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="56965a72-6fd7-4879-bb80-b72cb3af4a62" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5e07e272de044937cd6be7bfdbf2f4730aad10a9" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -42,7 +42,7 @@
 		</sample>
 	</sampleList>
 	<softwareList count="1">
-		<software id="Cardinal" version="2.4.0">
+		<software id="Cardinal" version="2.6.0">
 			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
 		</software>
 	</softwareList>
--- a/test-data/preprocessing_results5.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
+++ b/test-data/preprocessing_results5.imzml.txt	Tue Oct 06 08:12:49 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 428
--rw-r--r-- 1 meli meli 415936 Mai 10 17:40 ibd
--rw-r--r-- 1 meli meli  18569 Mai 10 17:40 imzml
+-rw-rw-r-- 1 meli meli 415936 Oct  5 19:59 ibd
+-rw-rw-r-- 1 meli meli  18569 Oct  5 19:59 imzml
Binary file test-data/preprocessing_results5.pdf has changed