profia: profia_config.xml comparison

comparison profia_config.xml @ 1:4753e64cf694 draft

planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51

author	ethevenot
date	Wed, 03 May 2017 10:49:08 -0400
parents	39ccace77270
children	3f8ae071bdda

comparison

equal deleted inserted replaced

-:39ccace77270
+:4753e64cf694
-<tool id="profia" name="proFIA" version="3.0.0">
+<tool id="profia" name="proFIA" version="3.0.4">
 <description>Preprocessing of FIA-HRMS data</description>
 <requirements>
 <requirement type="package">r-batch</requirement>
 <requirement type="package">r-FNN</requirement>
 <requirement type="package">r-maxLik</requirement>
 <requirement type="package">r-minpack.lm</requirement>
 <requirement type="package">r-pracma</requirement>
+<requirement type="package">bioconductor-xcms</requirement>
+<requirement type="package">bioconductor-plasFIA</requirement>
 <requirement type="package">bioconductor-proFIA</requirement>
 </requirements>
 <stdio>
 <exit_code range="1:" level="fatal" />
 </stdio>
-<command><![CDATA[
+<command>
 Rscript $__tool_directory__/profia_wrapper.R
 #if $inputs.input == "lib":
 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
 #elif $inputs.input == "zip_file":
 dataMatrix_out "$dataMatrix_out"
 sampleMetadata_out "$sampleMetadata_out"
 variableMetadata_out "$variableMetadata_out"
 figure "$figure"
 information "$information"
-]]></command>
+</command>
 <inputs>
 <conditional name="inputs">
 <param name="input" type="select" label="Choose your input method" >
 <option value="zip_file" selected="true">Zip file from your history containing your raw files</option>
 <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" >
 <validator type="empty_field"/>
 </param>
 <param name="inputs|zip_file" value="input-plasFIA.zip" ftype="zip" />
 <param name="ppmN" value="2"/>
 <param name="ppmGroupN" value="1"/>
 <param name="fracGroupN" value="0.1"/>
 <param name="kI" value="2"/>
-<output name="dataMatrix_out" file="output-dataMatrix.tsv"/>
+<output name="dataMatrix_out" file="output-dataMatrix.tsv" />
+<output name="information">
+<assert_contents>
+<has_text text="722  groups have been done" />
+	  <has_text text="3 samples x 644 variables" />
+	  <has_text text="78 excluded variables (near zero variance)" />
+<has_text text="2101  peaks detected" />
+</assert_contents>
+</output>
 </test>
 </tests>
 <help>
 .. class:: infomark
 **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*.
 ---------------------------------------------------
 .. class:: infomark
 See the **NEWS** section at the bottom of this page
 ---------------------------------------------------
 ==========================================================
-*proFIA*: Preprocessing workflow for FIA-HRMS data
+*proFIA*: A preprocessing workflow for FIA-HRMS data
 ==========================================================
 -----------
 Description
 -----------
 .. class:: infomark
 **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.
+| 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.
+| 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.
+| 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)
 ---------------------------------------------------
 -----------------
 Workflow position
 | Parameter : num + label   |   Format   |
 +===========================+============+
 | 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**
 **Step1: Creating your directory and hierarchize the subdirectories**
 .. 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
+1a) Prepare a parent folder with the name of your data set (e.g., 'arabidopsis') containing your files:
-arabidopsis/mutant/01.raw
+| '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.
+| 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).
+| 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).
+| 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**
 ----------
 Parameters
 ----------
 ----
 NEWS
 ----
+CHANGES IN VERSION 3.0.4
+========================
+MINOR MODIFICATION
+Details added in the documentation
+CHANGES IN VERSION 3.0.2
+========================
+NEW FEATURE
+Parallel processing
 CHANGES IN VERSION 3.0.0
 ========================
 NEW FEATURE
 </help>
 <citations>
 <citation type="bibtex">@Article{DelabriereSubmitted,
 Title                    = {proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry},
-Author                   = {Delabriere, Alexis and Hohenester, Ulli and Junot, Christophe and Thevenot, Etienne A},
+Author                   = {Delabriere, Alexis and Hohenester, Ulli and Colsch, Benoit and Junot, Christophe and Fenaille, Francois and Thevenot, Etienne A},
 Journal                  = {submitted},
 Year                     = {submitted},
 Pages                    = {--},
 Volume                   = {},
 Doi                      = {}

Mercurial > repos > ethevenot > profia

comparison profia_config.xml @ 1:4753e64cf694 draft