Mercurial > repos > lecorguille > xcms_xcmsset

changeset 4:4509e9dd03e4 draft

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planemo upload
author lecorguille
date Mon, 22 Feb 2016 16:59:10 -0500
parents 7366edf1b2cf
children b9a87af62223
files Makefile README.rst abims_xcms_xcmsSet.xml planemo.sh repository_dependencies.xml tool_dependencies.xml
diffstat 6 files changed, 147 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Makefile	Mon Feb 22 16:59:10 2016 -0500
@@ -0,0 +1,23 @@
+# USAGE: make [install|clean]
+
+# -------- VARIABLE --------
+
+OBJ=xcms_set.tgz
+DEP=abims_xcms_xcmsSet.xml tool_dependencies.xml repository_dependencies.xml static test-data
+
+
+# ------------------------
+
+all: $(OBJ)
+
+$(OBJ): $(DEP)
+	tar --exclude=".svn" -zchf $@ $^
+
+# ------------------------
+
+install: $(OBJ)
+	mv *.tgz ~
+
+clean:
+	rm *.tgz
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Feb 22 16:59:10 2016 -0500
@@ -0,0 +1,35 @@
+
+Changelog/News
+--------------
+
+
+**Version 2.0.7 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters
+
+- BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+- UPDATE: refactoring to feed the new report tool
+
+
+**Version 2.0.2 - 18/01/2016
+
+- BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
+
+
+**Version 2.0.2 - 09/10/2015**
+
+- BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows.
+
+
+**Version 2.0.2 - 02/06/2015**
+
+- NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible.
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
--- a/abims_xcms_xcmsSet.xml	Fri Jan 15 08:11:27 2016 -0500
+++ b/abims_xcms_xcmsSet.xml	Mon Feb 22 16:59:10 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.6">
+<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.7">
     
     <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
     
@@ -77,7 +77,7 @@
                 <option value="lib" >Library directory name</option>
             </param>
             <when value="zip_file">
-                <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />
+                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
              </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" >
@@ -304,6 +304,52 @@
     | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
     | 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**
+
+
+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
+
+**Step2: Creating a zip file**
+
+Create your zip file (e.g.: arabidopsis.zip).
+
+**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
+----------------------------------------------------
+
+We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method.
+
+**We recommend you 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
 ----------
@@ -412,6 +458,43 @@
 .. image:: xcms_tics.png
 
 
+---------------------------------------------------
+
+Changelog/News
+--------------
+
+
+**Version 2.0.7 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters
+
+- BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+- UPDATE: refactoring to feed the new report tool
+
+
+**Version 2.0.2 - 18/01/2016
+
+- BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
+
+
+**Version 2.0.2 - 09/10/2015**
+
+- BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows.
+
+
+**Version 2.0.2 - 02/06/2015**
+
+- NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible.
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
     ]]></help>
 
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo.sh	Mon Feb 22 16:59:10 2016 -0500
@@ -0,0 +1,1 @@
+planemo shed_init -f --name=xcms_xcms_set --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - peaks calling in NetCDF/mzXML files" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nFiltration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics"
--- a/repository_dependencies.xml	Fri Jan 15 08:11:27 2016 -0500
+++ b/repository_dependencies.xml	Mon Feb 22 16:59:10 2016 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories>
-    <repository changeset_revision="9ed593071db2" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="5527da68412e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 	<repository changeset_revision="bff835d58914" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
--- a/tool_dependencies.xml	Fri Jan 15 08:11:27 2016 -0500
+++ b/tool_dependencies.xml	Mon Feb 22 16:59:10 2016 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R" version="3.1.2">
-        <repository changeset_revision="73cd1d529330" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="xcms" version="1.44.0">
         <repository changeset_revision="8ea252413ed6" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="xcms_w4m_script" version="2.2.0">
-        <repository changeset_revision="e0d3e1caf5d9" name="package_xcms_w4m_script_2_2_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="f54521c7a50c" name="package_xcms_w4m_script_2_2_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>