diff ipo4xcmsSet.xml @ 3:9f1e18bc8ce3 draft

planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipo4xcmsSet.xml	Thu Jul 28 11:03:04 2016 -0400
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+<tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="2.0.8">
+    
+    <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    
+    <command><![CDATA[
+        @COMMAND_SCRIPT@
+
+        #if $inputs.input == "zip_file":
+            zipfile $inputs.zip_file
+        #elif $inputs.input == "single_file":
+            singlefile_galaxyPath $inputs.single_file singlefile_sampleName $inputs.single_file.name
+        #end if
+
+        parametersOutput $parametersOutput
+
+        samplebyclass $samplebyclass
+
+        ## profmethod $profmethod 
+        nSlaves \${GALAXY_SLOTS:-1} method $methods.method 
+        #if $methods.method == "centWave":
+            ppm $methods.ppm
+            min_peakwidth "c($methods.min_peakwidth)"
+            max_peakwidth "c($methods.max_peakwidth)"
+        #elif $methods.method == "matchedFilter":
+            step $methods.step
+            fwhm $methods.fwhm
+        #end if
+
+        @COMMAND_LOG_EXIT@ 2> /tmp/log.err
+    ]]></command>
+    
+    <inputs>
+
+        <conditional name="inputs">
+            <param name="input" type="select" label="Choose your inputs method" >
+                <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
+                <option value="single_file">mzXML file from your history</option>
+            </param>
+            <when value="zip_file">
+                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
+            </when>
+            <when value="single_file">
+                <param name="single_file" type="data" format="mzxml" label="Single file" />
+            </when>
+        </conditional>
+        
+        <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" />
+
+        <conditional name="methods">
+            <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
+                <option value="centWave" >centWave</option>
+                <option value="matchedFilter" selected="true">matchedFilter</option>
+            </param>
+
+            <!-- centWave Filter options -->
+            <when value="centWave">
+                <param name="ppm" type="text" value="5,25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" optional="false" />
+                <param name="min_peakwidth" type="text" value="15,25" label="Min peak width range in seconds" help="[peakwidth]" optional="true" />
+                <param name="max_peakwidth" type="text" value="45,55" label="Max peak width range in seconds" help="[peakwidth]" optional="true" />
+            </when>
+
+            <!-- matched Filter options -->
+            <when value="matchedFilter">
+                <param name="step" type="float" value="0.01" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" optional="true" />
+                <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" optional="true" />
+            </when>
+        </conditional>       
+
+
+    </inputs>
+    
+    <outputs>
+        <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" />
+        <data name="log" format="txt" label="ipo4xcmsSet.log.txt" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="inputs|input" value="single_file" />
+            <param name="inputs|single_file" value="MM14.mzML"  ftype="mzxml" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="56" />
+            <param name="methods|min_peakwidth" value="3,9.5" />
+            <param name="methods|max_peakwidth" value="10,20" />
+            <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet.tsv" />
+        </test>
+        <!--Failed:
+                Error in resultIncreased(history) : 
+                        No isotopes have been detected, peak picking not optimizable by IPO!-->
+        <!--<test>
+            <param name="inputs|input" value="zip_file" />
+            <param name="inputs|zip_file" value="sacuri_2files.zip"  ftype="zip" />
+            <param name="samplebyclass" value="1" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="25" />
+            <param name="methods|min_peakwidth" value="20,30" />
+            <param name="methods|max_peakwidth" value="45,55" />
+            <output name="parametersOutput" file="sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv" />
+        </test>-->
+        <!-- Too long for Travis CI -->
+        <!--<test>
+            <param name="inputs|input" value="zip_file" />
+            <param name="inputs|zip_file" value="sacuri_2files.zip"  ftype="zip" />
+            <param name="samplebyclass" value="1" />
+            <param name="methods|method" value="matchedFilter" />
+            <param name="methods|step" value="0.01" />
+            <param name="methods|fwhm" value="4" />
+            <output name="parametersOutput" file="sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv" />
+        </test>-->
+    </tests>
+    
+    <help><![CDATA[
+
+@HELP_AUTHORS@
+
+===============
+IPO.ipo4xcmsSet
+===============
+
+-----------
+Description
+-----------
+
+A Tool for automated Optimization of XCMS Parameters
+
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+========================= ================= ======= =========
+Name                      output file       format  parameter
+========================= ================= ======= =========
+NA                        NA                zip     NA       
+========================= ================= ======= =========
+
+
+**Downstream tools**
+
++---------------------------+----------------------+-----------------+
+| Name                      | Output file          | Format          |
++===========================+======================+=================+
+|xcms.xcmsSet               | parametersOutput.tsv | Tabular         |
++---------------------------+--------------------+-------------------+
+
+
+
+-----------
+Input files
+-----------
+
++---------------------------+------------+
+| Parameter : num + label   |   Format   |
++===========================+============+
+| 1 : Choose your inputs    |   zip      |
++---------------------------+------------+
+
+**Choose your inputs**
+
+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).
+    | 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
+----------
+
+Extraction method for peaks detection
+-------------------------------------
+
+**Matched Filter**
+
+    | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. 
+    | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
+
+
+**cent Wave**
+
+    | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
+    | Due to the fact that peak centroids are used, a binning step is not necessary.
+    | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals.
+
+
+------------
+Output files
+------------
+
+IPO_parameters4xcmsSet.tsv
+
+    | Optimal parameters for xcmsSet
+
+
+---------------------------------------------------
+
+Changelog/News
+--------------
+
+
+
+    ]]></help>
+
+    <expand macro="citation" />
+</tool>