Mercurial > repos > lecorguille > msnbase_readmsdata

changeset 10:84533814b1d5 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
author lecorguille
date Mon, 29 Apr 2019 06:07:14 -0400
parents 3d8a68b45153
children 144392dd4a31
files README.rst lib.r macros_msnbase.xml msnbase_readmsdata.r msnbase_readmsdata.xml
diffstat 5 files changed, 27 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Apr 29 06:07:14 2019 -0400
@@ -0,0 +1,11 @@
+
+Changelog/News
+--------------
+
+**Version 2.8.2.0 - 08/04/2019**
+
+- UPGRADE: upgrade the MSnbase version from 2.4.0 to 2.8.2 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase.
+
+**Version 2.4.0.0 - 29/03/2018**
+
+- NEW: a new dedicated tool to read the raw data. This function was previously included in xcms.findChromPeaks. This way, you will now be able to display TICs and BPCs before xcms.findChromPeaks.
--- a/lib.r	Fri Feb 08 09:55:50 2019 -0500
+++ b/lib.r	Mon Apr 29 06:07:14 2019 -0400
@@ -69,7 +69,7 @@
             chromBPI_adjusted_merged <- chromBPI_adjusted
         } else {
             if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
-            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
+            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata)
             else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
 
             singlefile_merged <- c(singlefile_merged,singlefile)
@@ -333,7 +333,7 @@
     files[exists] <- sub("//","/",files[exists])
 
     # WHAT IS ON THE FILESYSTEM
-    filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
+    filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
     filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
 
     # COMPARISON
--- a/macros_msnbase.xml	Fri Feb 08 09:55:50 2019 -0500
+++ b/macros_msnbase.xml	Mon Apr 29 06:07:14 2019 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@WRAPPER_VERSION@">2.4.0</token>
+    <token name="@WRAPPER_VERSION@">2.8.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-msnbase</requirement>
--- a/msnbase_readmsdata.r	Fri Feb 08 09:55:50 2019 -0500
+++ b/msnbase_readmsdata.r	Mon Apr 29 06:07:14 2019 -0400
@@ -91,7 +91,7 @@
 cat("\n\n")
 
 #saving R data in .Rdata file to save the variables used in the present tool
-objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList", "chromTIC", "chromBPI")
+objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI")
 save(list=objects2save[objects2save %in% ls()], file="readmsdata.RData")
 
 
--- a/msnbase_readmsdata.xml	Fri Feb 08 09:55:50 2019 -0500
+++ b/msnbase_readmsdata.xml	Mon Apr 29 06:07:14 2019 -0400
@@ -42,7 +42,7 @@
                 <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" />
                 <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" />
                 <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" />
-                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" />
+                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" />
                 <has_text text="faahKO_reduce/KO/ko15.CDF        ko15           KO" />
                 <has_text text="faahKO_reduce/KO/ko16.CDF        ko16           KO" />
                 <has_text text="faahKO_reduce/WT/wt15.CDF        wt15           WT" />
@@ -56,12 +56,12 @@
                 <has_text text="rowNames: ./ko15.CDF" />
                 <has_text text="ko15.CDF" />
                 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" />
-                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" />
+                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" />
                 <has_text text="./ko15.CDF        ko15            ." />
             </assert_stdout>
         </test>
         <!-- DISABLE FOR TRAVIS
-        Useful to generate test-data for the further steps-->
+        Useful to generate test-data for the further steps
         <test>
             <param name="input" value="ko16.CDF"  ftype="netcdf" />
             <assert_stdout>
@@ -86,7 +86,7 @@
                 <has_text text="./wt16.CDF        wt16            ." />
             </assert_stdout>
         </test>
-        <!-- -->
+        -->
     </tests>
 
     <help><![CDATA[
@@ -132,7 +132,7 @@
 xcms.findChromPeaks         ``*``.raw.RData      rdata.msnbase.raw
 =========================== ==================== ====================
 
- 
+
 
 **Example of a metabolomic workflow**
 
@@ -158,7 +158,7 @@
 
 You have two methods for your inputs:
 
-    | Single file (recommended): You can put a single file as input. That way, you will be able to launch several readMSData and findChromPeaks in parallel and use "findChromPeaks Merger" before groupChromPeaks. 
+    | Single file (recommended): You can put a single file as input. That way, you will be able to launch several readMSData and findChromPeaks in parallel and use "findChromPeaks Merger" before groupChromPeaks.
     | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
 
 Zip file: Steps for creating the zip file
@@ -223,13 +223,18 @@
 
     | Tabular file that contains for each sample its associated class and polarity (positive,negative and mixed).
     | This file is necessary in further steps of the workflow, as the Anova and PCA steps for example.
-    | You get a sampleMetadata.tsv only if you use a zip. Otherwise, you have to provide one for the findChromPeaks Merger step. 
+    | You get a sampleMetadata.tsv only if you use a zip. Otherwise, you have to provide one for the findChromPeaks Merger step.
 
 ---------------------------------------------------
 
 Changelog/News
 --------------
 
+.. _News: https://bioconductor.org/packages/release/bioc/news/MSnbase/NEWS
+
+**Version 2.8.2.0 - 08/04/2019**
+
+- UPGRADE: upgrade the MSnbase version from 2.4.0 to 2.8.2 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase.
 
 **Version 2.4.0.0 - 29/03/2018**