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changeset 1:bc95bcb6ead0 draft

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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
author ethevenot
date Wed, 03 May 2017 10:39:00 -0400
parents c135ba23a2a3
children e29c563df582
files README.md profia_config.xml profia_wrapper.R runit/output/figure.pdf runit/output/information.txt runit/output/sampleMetadata.tsv
diffstat 6 files changed, 61 insertions(+), 41 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Sat Apr 22 07:27:42 2017 -0400
+++ b/README.md	Wed May 03 10:39:00 2017 -0400
@@ -7,8 +7,8 @@
 
 ### Description
 
-**Version:** 3.0.2  
-**Date:** 2017-04-21     
+**Version:** 3.0.4  
+**Date:** 2017-05-02     
 **Author:** Alexis Delabriere and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)   
 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)  
 **Citation:** Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*.   
@@ -55,6 +55,12 @@
 
 ### News
 
+###### CHANGES IN VERSION 3.0.4  
+
+MINOR MODIFICATION  
+
+ * Details added in the documentation  
+
 ###### CHANGES IN VERSION 3.0.2  
 
 NEW FEATURE  
--- a/profia_config.xml	Sat Apr 22 07:27:42 2017 -0400
+++ b/profia_config.xml	Wed May 03 10:39:00 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="profia" name="proFIA" version="3.0.2">
+<tool id="profia" name="proFIA" version="3.0.4">
   <description>Preprocessing of FIA-HRMS data</description>
   
   <requirements>
@@ -44,7 +44,7 @@
         <option value="lib" >Library directory name</option>
       </param>
       <when value="zip_file">
-        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
+        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file (see the details for file upload in the help section below)" />
       </when>
       <when value="lib">
         <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
@@ -99,7 +99,7 @@
 
 **Please cite**
 
-Delabriere A., Hohenester U., Junot C. and Thevenot E.A. *proFIA*: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*.
+Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. *proFIA*: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*.
 
 ---------------------------------------------------
 
@@ -120,7 +120,7 @@
 ---------------------------------------------------
 
 ==========================================================
-*proFIA*: Preprocessing workflow for FIA-HRMS data
+*proFIA*: A preprocessing workflow for FIA-HRMS data
 ==========================================================
 
 -----------
@@ -142,9 +142,9 @@
 **References**
 
 | Delabriere A., Hohenester U., Junot C. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*.
-| Draper J., Lloyd A., Goodacre R. and Beckmann M. (2013). Flow infusion electrospray ionisation mass spectrometry for high throughput, non-targeted metabolite fingerprinting: a review. *Metabolomics* 9, 4-29.
-| Fuhrer T., Dominik H., Boris B. and Zamboni N. (2011). High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry. *Analytical Chemistry* 83, 7074-7080.
-| Madalinski G., Godat E., Alves S., Lesage D., Genin E., Levi P., Labarre J., Tabet J., Ezan E. and Junot, C. (2008). Direct introduction of biological samples into a LTQ-orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. *Analytical Chemistry* 80, 3291-3303.
+| Draper J., Lloyd A., Goodacre R. and Beckmann M. (2013). Flow infusion electrospray ionisation mass spectrometry for high throughput, non-targeted metabolite fingerprinting: a review. *Metabolomics* 9, 4-29. (http://dx.doi.org/10.1007/s11306-012-0449-x)
+| Fuhrer T., Dominik H., Boris B. and Zamboni N. (2011). High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry. *Analytical Chemistry* 83, 7074-7080. (http://dx.doi.org/10.1021/ac201267k)
+| Madalinski G., Godat E., Alves S., Lesage D., Genin E., Levi P., Labarre J., Tabet J., Ezan E. and Junot, C. (2008). Direct introduction of biological samples into a LTQ-orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. *Analytical Chemistry* 80, 3291-3303. (http://dx.doi.org/10.1021/ac7024915)
 
 ---------------------------------------------------
 
@@ -165,9 +165,15 @@
 | 1 : Choose your inputs    |   zip      |
 +---------------------------+------------+
 
+---------------------------------------------------
+
+.. class:: warningmark
+
+VERY IMPORTANT: Your data must be in **centroid** mode (centroidization of raw files and conversion to an open format can be achieved with the proteowizard software: http://proteowizard.sourceforge.net/).
+
 
 You have two methods for your inputs:
-    | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
+    | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories; see below).
     | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.
 
 **Steps for creating the zip file**
@@ -177,33 +183,34 @@
 .. class:: warningmark
 
 VERY IMPORTANT: If you zip your files under Windows, you must use the **7Zip** software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).
-Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
-arabidopsis/wild/01.raw
-arabidopsis/mutant/01.raw
 
+1a) Prepare a parent folder with the name of your data set (e.g., 'arabidopsis') containing your files:
+   | 'arabidopsis/w1.raw'
+   | 'arabidopsis/w2.raw'
+   | ...
+   | 'arabidopsis/m1.raw'
+   | 'arabidopsis/m2.raw'
+   | ...
+   |
+   
+1b) If you have several experimental conditions resulting in distinct profiles of your samples (e.g. 'wild-type' and 'mutant' genotypes), create subfolders for your files (e.g., 'wild' and 'mutant') into your parent folder:
+   | 'arabidopsis/wild/w1.raw'
+   | 'arabidopsis/wild/w2.raw'
+   | ...
+   | 'arabidopsis/mutant/m1.raw'
+   | 'arabidopsis/mutant/m2.raw'
+   | ...
+   |
+   
 **Step2: Creating a zip file**
-Create your zip file (e.g.: arabidopsis.zip).
+   | Zip your **parent** folder (here the 'arabidopsis' folder) containing all the subfolders and files with **7Zip**.
+   |
 
 **Step 3 : Uploading it to our Galaxy server**
-If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
-Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).
-For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
-
-**Advices for converting your files for the XCMS input**
-
-.. class:: warningmark
-
-VERY IMPORTANT: your data must be in **centroid** mode. In addition, we recommend you to convert your raw files to mzXML.
-
-We recommend the following parameters:
-
-Use Filtering: **True**
-Use Peak Picking: **True**
-Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
-Use zlib: **64**
-Binary Encoding: **64**
-m/z Encoding: **64**
-Intensity Encoding: **64**
+   | If your zip file is less than 2Gb, you get use the **Upload File** tool and the **no_unzip.zip** type to upload it.
+   | Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).
+   | For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
+   |
 
 ----------
 Parameters
@@ -268,6 +275,13 @@
 NEWS
 ----
 
+CHANGES IN VERSION 3.0.4
+========================
+
+MINOR MODIFICATION
+
+Details added in the documentation
+
 CHANGES IN VERSION 3.0.2
 ========================
 
--- a/profia_wrapper.R	Sat Apr 22 07:27:42 2017 -0400
+++ b/profia_wrapper.R	Wed May 03 10:39:00 2017 -0400
@@ -182,8 +182,8 @@
             row.names = FALSE,
             sep = "\t")
 
-samDF <- cbind.data.frame(sampleMetadata = rownames(samDF),
-                          samDF)
+samDF <- cbind.data.frame(sampleMetadata = samDF[, "sampleID"],
+                          class = samDF[, "class"])
 write.table(samDF,
             file = argVc["sampleMetadata_out"],
             quote = FALSE,
Binary file runit/output/figure.pdf has changed
--- a/runit/output/information.txt	Sat Apr 22 07:27:42 2017 -0400
+++ b/runit/output/information.txt	Wed May 03 10:39:00 2017 -0400
@@ -1,5 +1,5 @@
 
-Start of the 'proFIA' Galaxy module call: Fri 21 Apr 2017 09:13:07 PM
+Start of the 'proFIA' Galaxy module call: Wed 03 May 2017 01:18:28 PM
 files_root_directory	 plasFIA 
 
 1) Peak detection step ('proFIAset'):
@@ -32,4 +32,4 @@
 
 7) Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):
 
-End of 'proFIA' Galaxy module call: 2017-04-21 21:14:58
+End of 'proFIA' Galaxy module call: 2017-05-03 13:27:09
--- a/runit/output/sampleMetadata.tsv	Sat Apr 22 07:27:42 2017 -0400
+++ b/runit/output/sampleMetadata.tsv	Wed May 03 10:39:00 2017 -0400
@@ -1,4 +1,4 @@
-sampleMetadata	sampleID	class
-1	C100a	plasFIA
-2	C100b	plasFIA
-3	C100c	plasFIA
+sampleMetadata	samDF[, colnames(samDF) != "sampleID"]
+C100a	plasFIA
+C100b	plasFIA
+C100c	plasFIA