Mercurial > repos > lecorguille > xcms_xcmsset

changeset 5:588b0a7ae4b0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author lecorguille
date Mon, 22 Feb 2016 16:25:05 -0500
parents c5fa73f1703f
children 0888f7ef739a
files README.rst abims_xcms_xcmsSet.xml test-data/log.txt test-data/xset.log.txt tool_dependencies.xml
diffstat 5 files changed, 221 insertions(+), 84 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Feb 22 16:25:05 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	Tue Nov 24 06:06:30 2015 -0500
+++ b/abims_xcms_xcmsSet.xml	Mon Feb 22 16:25:05 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.2">
+<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>
     
@@ -6,14 +6,14 @@
         <requirement type="package" version="3.1.2">R</requirement>
         <requirement type="binary">Rscript</requirement>
         <requirement type="package" version="1.44.0">xcms</requirement>
-        <requirement type="package" version="2.1">xcms_w4m_script</requirement>
+        <requirement type="package" version="2.2.0">xcms_w4m_script</requirement>
     </requirements>
     
     <stdio>
         <exit_code range="1:" level="fatal" />
     </stdio>
     
-    <command>
+    <command><![CDATA[
         xcms.r
         #if $inputs.input == "lib":
             library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
@@ -22,6 +22,12 @@
         #end if
 
         xfunction xcmsSet
+
+        xsetRdataOutput $xsetRData
+        sampleMetadataOutput $sampleMetadata
+        ticspdf $ticsRawPdf
+        bicspdf $bpcsRawPdf
+
         ## profmethod $profmethod 
         nSlaves \${GALAXY_SLOTS:-1} method $methods.method 
         #if $methods.method == "centWave":
@@ -29,14 +35,14 @@
             peakwidth "c($methods.peakwidth)"
         #if $methods.options_scanrange.option == "show":
                 scanrange "c($methods.options_scanrange.scanrange)"
-            #end if 
-            #if $methods.options_c.option == "show":
-                mzdiff $methods.options_c.mzdiff
-                snthresh $methods.options_c.snthresh
-                integrate $methods.options_c.integrate
-                noise $methods.options_c.noise
-                prefilter "c($methods.options_c.prefilter)"
-            #end if
+        #end if 
+        #if $methods.options_c.option == "show":
+            mzdiff $methods.options_c.mzdiff
+            snthresh $methods.options_c.snthresh
+            integrate $methods.options_c.integrate
+            noise $methods.options_c.noise
+            prefilter "c($methods.options_c.prefilter)"
+        #end if
         #elif $methods.method == "matchedFilter":
             step $methods.step
             fwhm $methods.fwhm
@@ -56,13 +62,12 @@
             scales "c($methods.scales)"
             SNR.method "$methods.SNR_method"
         #end if
-        &amp;&amp; (mv xcmsSet.RData $xsetRData;
-        mv sampleMetadata.tsv $sampleMetadata;
-        mv TICs_raw.pdf $ticsRawPdf;
-        mv BPCs_raw.pdf $bpcsRawPdf;
-        mv xset.log $log);
-        cat $log
-    </command>
+        ;
+        return=\$?;
+        mv log.txt $log;
+        cat $log;
+        sh -c "exit \$return"
+    ]]></command>
     
     <inputs>
 
@@ -72,7 +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" >
@@ -113,6 +118,8 @@
                             <validator type="empty_field"/> 
                         </param>
                     </when>
+                    <when value="hide">
+                    </when>
                 </conditional>
                         
                 <conditional name="options_c">
@@ -130,6 +137,8 @@
                         <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/>
                         <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/>
                     </when>
+                    <when value="hide">
+                    </when>
                 </conditional>
             </when>
 
@@ -153,6 +162,8 @@
                         <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " />
 -->
                     </when>
+                    <when value="hide">
+                    </when>
                 </conditional>
             </when>
 
@@ -190,15 +201,24 @@
             <param name="methods.options_m.max" value="50" />
             <param name="methods.options_m.snthresh" value="1" />
             <param name="methods.options_m.steps" value="2" />
-            <output name="xsetRData" file="xset.RData" />
-            <output name="sampleMetadata" file="sampleMetadata.tsv" />
-            <output name="ticsRawPdf" file="xset.TICs_raw.pdf" />
-            <output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />
-            <output name="log" file="xset.log.txt" />
+            <!--<output name="xsetRData" file="xset.RData" />-->
+            <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />-->
+            <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />-->
+            <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />-->
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 9 samples" />
+                    <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" />
+                    <has_text text="Mass range: 50.0019-999.9863 m/z" />
+                    <has_text text="Peaks: 135846 (about 15094 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: bio, blank" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     
-    <help>
+    <help><![CDATA[
 
 .. class:: infomark
 
@@ -284,6 +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
 ----------
@@ -392,8 +458,44 @@
 .. image:: xcms_tics.png
 
 
+---------------------------------------------------
 
-    </help>
+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>
 
 
     <citations>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log.txt	Mon Feb 22 16:25:05 2016 -0500
@@ -0,0 +1,56 @@
+	PACKAGE INFO
+parallel	3.1.1
+BiocGenerics	0.12.1
+Biobase	2.26.0
+Rcpp	0.11.5
+mzR	2.0.0
+igraph	0.7.1
+xcms	1.42.0
+snow	0.3.13
+batch	1.1.4
+
+
+	ARGUMENTS INFO
+zipfile	/w/galaxy/galaxy4metabolomics/galaxy-dist/database/files/041/dataset_41794.dat
+xfunction	xcmsSet
+nSlaves	8
+method	matchedFilter
+step	0.01
+fwhm	4
+max	50
+snthresh	1
+steps	2
+
+
+	INFILE PROCESSING INFO
+
+
+	MAIN PROCESSING INFO
+Starting snow cluster with 8 local sockets.
+Detecting features in file # 1 : HU_neg_028.mzXML 
+Detecting features in file # 2 : HU_neg_060.mzXML 
+Detecting features in file # 3 : HU_neg_051.mzXML 
+Detecting features in file # 4 : HU_neg_017.mzXML 
+Detecting features in file # 5 : HU_neg_034.mzXML 
+Detecting features in file # 6 : Blanc09.mzXML 
+Detecting features in file # 7 : Blanc06.mzXML 
+Detecting features in file # 8 : Blanc12.mzXML 
+Detecting features in file # 9 : Blanc04.mzXML 
+
+
+	XSET OBJECT INFO
+An "xcmsSet" object with 9 samples
+
+Time range: 0.7-1140 seconds (0-19 minutes)
+Mass range: 50.0019-999.9863 m/z
+Peaks: 135846 (about 15094 per sample)
+Peak Groups: 0 
+Sample classes: bio, blank 
+
+Profile settings: method = bin
+                  step = 0.01
+
+Memory usage: 13.8 MB
+
+
+	DONE
--- a/test-data/xset.log.txt	Tue Nov 24 06:06:30 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-	PACKAGE INFO
-parallel	3.1.1
-BiocGenerics	0.12.1
-Biobase	2.26.0
-Rcpp	0.11.5
-mzR	2.0.0
-igraph	0.7.1
-xcms	1.42.0
-snow	0.3.13
-batch	1.1.4
-
-
-	ARGUMENTS INFO
-zipfile	/w/galaxy/galaxy4metabolomics/galaxy-dist/database/files/041/dataset_41794.dat
-xfunction	xcmsSet
-nSlaves	8
-method	matchedFilter
-step	0.01
-fwhm	4
-max	50
-snthresh	1
-steps	2
-
-
-	INFILE PROCESSING INFO
-
-
-	MAIN PROCESSING INFO
-Starting snow cluster with 8 local sockets.
-Detecting features in file # 1 : HU_neg_028.mzXML 
-Detecting features in file # 2 : HU_neg_060.mzXML 
-Detecting features in file # 3 : HU_neg_051.mzXML 
-Detecting features in file # 4 : HU_neg_017.mzXML 
-Detecting features in file # 5 : HU_neg_034.mzXML 
-Detecting features in file # 6 : Blanc09.mzXML 
-Detecting features in file # 7 : Blanc06.mzXML 
-Detecting features in file # 8 : Blanc12.mzXML 
-Detecting features in file # 9 : Blanc04.mzXML 
-
-
-	XSET OBJECT INFO
-An "xcmsSet" object with 9 samples
-
-Time range: 0.7-1140 seconds (0-19 minutes)
-Mass range: 50.0019-999.9863 m/z
-Peaks: 135846 (about 15094 per sample)
-Peak Groups: 0 
-Sample classes: bio, blank 
-
-Profile settings: method = bin
-                  step = 0.01
-
-Memory usage: 13.8 MB
-
-
-	DONE
--- a/tool_dependencies.xml	Tue Nov 24 06:06:30 2015 -0500
+++ b/tool_dependencies.xml	Mon Feb 22 16:25:05 2016 -0500
@@ -6,7 +6,7 @@
     <package name="xcms" version="1.44.0">
         <repository changeset_revision="4443617bdd85" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="xcms_w4m_script" version="2.1">
-        <repository changeset_revision="c94c8ef520c8" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="xcms_w4m_script" version="2.2.0">
+        <repository changeset_revision="115cf2b43a3c" name="package_xcms_w4m_script_2_2_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>