Mercurial > repos > lecorguille > ipo
diff ipo4retgroup.xml @ 6:03fdfbd914ab draft
planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
| author | lecorguille |
|---|---|
| date | Thu, 30 Mar 2017 11:27:09 -0400 |
| parents | |
| children | dd0a593dded1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipo4retgroup.xml Thu Mar 30 11:27:09 2017 -0400 @@ -0,0 +1,377 @@ +<tool id="ipo4retgroup" name="IPO for group and retcor" version="0.0.1"> + + <description>IPO optimization process for xcms.group and xcms.retcor</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + <command><![CDATA[ + LANG=C Rscript $__tool_directory__/ipo4retgroup.r + + image '$image' + + parametersOutput '$parametersOutput' + + samplebyclass $samplebyclass + + @COMMAND_NSLAVES@ + + ## group methods + + sleep 0.001 + #if $group.methods.method == "density": + bw "c($group.methods.bw)" + minfrac "c($group.methods.minfrac)" + mzwid "c($group.methods.mzwid)" + ## minsamp "c($group.methods.minsamp)" + #if $group.methods.density_options.option == "show": + max "c($group.methods.density_options.max)" + #end if + #end if + + + + ## retcor methods + + #if $retcor.methods.method == "obiwarp": + retcorMethod obiwarp + profStep "c($methods.profStep)" + + ## $distFunc [1] "cor_opt" + ## $gapInit [1] 0.0 0.4 + ## $gapExtend [1] 2.1 2.7 + ## $$plottype [1] "none" + ## $response [1] 1 + ## $factorDiag [1] 2 + ## $factorGap [1] 1 + ## $localAlignment [1] 0 + + #elif $retcor.methods.method == "peakgroups": + ## smooth loess + retcorMethod loess + smooth loess + extra "c($retcor.methods.extra)" + missing "c($retcor.methods.missing)" + #if $retcor.methods.options.option == "show": + span "c($retcor.methods.options.span)" + family "$retcor.methods.options.family" + plottype "$retcor.methods.options.plottype" + #end if + #elif $retcor.methods.method == "none": + retcorMethod none + #end if + + @COMMAND_FILE_LOAD@ + + @COMMAND_LOG_EXIT@ + ]]></command> + + <inputs> + + <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> + + <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" /> + + <section name="group" title="Group Options" expanded="False"> + + <conditional name="methods"> + <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below"> + <option value="density" selected="true">density</option> + </param> + <when value="density"> + <param name="bw" type="text" value="22,38" label="Range for Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram (ex: 30 or 22,38)" /> + <param name="minfrac" type="text" value="0.3,0.7" label="Range for Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group (ex: 0.5 or 0.3,0.7)" /> + <param name="mzwid" type="text" value="0.015,0.035" label="Range for Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples (ex: 0.25 or 0.015,0.035)" /> + <!-- + <param name="minsamp" type="hidden" value="1" label="Range for Minimum number of samples necessary in at least one of the sample groups for it to be a valid group" help="[minsamp] (ex: 1 or 0,5" /> + --> + <conditional name="density_options"> + <param name="option" type="select" label="Advanced options"> + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="max" type="text" value="50" label="Range for Maximum number of groups to identify in a single m/z slice" help="[max] (ex: 50 or 25,75)" /> + </when> + <when value="hide"> + </when> + </conditional> + + </when> + </conditional> + + + </section> + + <section name="retcor" title="Retcor Options" expanded="False"> + <conditional name="methods"> + <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" > + <option value="obiwarp">obiwarp</option> + <option value="peakgroups">peakgroups</option> + </param> + <when value="obiwarp"> + <param name="profStep" type="text" value="0.7,1.0" label="Range for Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files (ex: 1 or 0.7 1.0)" /> + <!-- + ## $distFunc [1] "cor_opt" + ## $gapInit [1] 0.0 0.4 + ## $gapExtend [1] 2.1 2.7 + ## $$plottype [1] "none" + ## $response [1] 1 + ## $factorDiag [1] 2 + ## $factorGap [1] 1 + ## $localAlignment [1] 0 + --> + </when> + <when value="peakgroups"> + <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" > + <option value="loess">loess</option> + </param> + <param name="extra" type="text" value="1" label="Range for Number of extra peaks to allow in retention time correction correction groups" help="[extra] (ex: 1 or 1,3)" /> + <param name="missing" type="text" value="1" label="Range for Number of missing samples to allow in retention time correction groups" help="[missing] (ex: 1or 1,3)" /> + + <conditional name="options"> + <param name="option" type="select" label="Advanced options"> + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="span" type="text" value="0.1,0.3" label="Range for Degree of smoothing for local polynomial regression fitting" help="[span] (ex: 0.2 or 0.1,0.3)"/> + <!-- @TODO multiple="true" --> + <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> + <option value="gaussian" selected="true">gaussian</option> + <option value="symmetric">symmetric</option> + </param> + <!-- @TODO multiple="true" --> + <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> + <option value="none" selected="true">none</option> + <option value="deviation">deviation</option> + <option value="mdevden">mdevden</option> + </param> + + </when> + <when value="hide"> + </when> + </conditional> + </when> + </conditional> + + </section> + + <expand macro="file_load"/> + + </inputs> + + <outputs> + <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" /> + <data name="log" format="txt" label="ipo4xcmsSet.log.txt" /> + </outputs> + + <tests> + <!-- TOO LONG + <test> + <param name="image" value="faahKO.xset.RData"/> + <param name="group|methods|method" value="density"/> + <param name="group|methods|bw" value="28,32"/> + <param name="group|methods|minfrac" value="1"/> + <param name="group|methods|mzwid" value="0.15,0.35"/> + <param name="retcor|methods|method" value="peakgroups"/> + <param name="retcor|methods|smooth" value="loess"/> + <param name="retcor|methods|extra" value="1"/> + <param name="retcor|methods|missing" value="1"/> + <param name="file_load_conditional|file_load_select" value="yes" /> + <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup.tsv" /> + </test>--> + + <test> + <param name="image" value="faahKO.xset.RData"/> + <param name="group|methods|method" value="density"/> + <param name="group|methods|bw" value="28,32"/> + <param name="group|methods|minfrac" value="1"/> + <param name="group|methods|mzwid" value="0.25"/> + <param name="retcor|methods|method" value="peakgroups"/> + <param name="retcor|methods|smooth" value="loess"/> + <param name="retcor|methods|extra" value="1"/> + <param name="retcor|methods|missing" value="1"/> + <param name="file_load_conditional|file_load_select" value="yes" /> + <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_bw.tsv" /> + </test> + + <test> + <param name="image" value="faahKO.xset.RData"/> + <param name="group|methods|method" value="density"/> + <param name="group|methods|bw" value="30"/> + <param name="group|methods|minfrac" value="1"/> + <param name="group|methods|mzwid" value="0.15,0.35"/> + <param name="retcor|methods|method" value="peakgroups"/> + <param name="retcor|methods|smooth" value="loess"/> + <param name="retcor|methods|extra" value="1"/> + <param name="retcor|methods|missing" value="1"/> + <param name="file_load_conditional|file_load_select" value="yes" /> + <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_mzmid.tsv" /> + </test> + + <!--<test> + <param name="image" value="MM-xset-merge.RData"/> + <param name="group|methods|method" value="density"/> + <param name="group|methods|bw" value="22,38"/> + <param name="group|methods|minfrac" value="1"/> + <param name="group|methods|mzwid" value="0.015,0.035"/> + <param name="retcor|methods|method" value="peakgroups"/> + <param name="retcor|methods|smooth" value="loess"/> + <param name="retcor|methods|extra" value="1"/> + <param name="retcor|methods|missing" value="1"/> + <param name="file_load_conditional|file_load_select" value="yes" /> + <param name="file_load_conditional|inputs|input" value="single_file" /> + <param name="file_load_conditional|inputs|single_file" value="MM8.mzML,MM14.mzML" ftype="mzxml" /> + <output name="parametersOutput" file="MM_IPO_parameters4retgroup.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>