--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipo4retgroup.xml	Thu Aug 03 06:00:00 2017 -0400
@@ -0,0 +1,364 @@
+<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>
+
+        <macro name="group_density_bw_fixed">
+            <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />
+        </macro>
+
+        <macro name="group_density_mzwid_fixed">
+            <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />
+        </macro>
+    </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.section_group_density_optiomizable.conditional_parameter.bw)"
+            mzwid "c($group.methods.section_group_density_optiomizable.conditional_parameter.mzwid)"
+
+            minfrac $group.methods.section_group_density_non_optimizable.minfrac
+            max $group.methods.section_group_density_non_optimizable.max
+        #end if
+
+        ## retcor methods
+
+        #if $retcor.methods.method == "obiwarp":
+            retcorMethod obiwarp
+            profStep $methods.section_retcor_obiwarp_non_optimizable.profStep
+
+        #elif $retcor.methods.method == "peakgroups":
+            retcorMethod loess
+            smooth $retcor.methods.section_retcor_peakgroups_non_optimizable.smooth
+            extra $retcor.methods.section_retcor_peakgroups_non_optimizable.extra
+            missing $retcor.methods.section_retcor_peakgroups_non_optimizable.missing
+            span $retcor.methods.section_retcor_peakgroups_non_optimizable.span
+            family $retcor.methods.section_retcor_peakgroups_non_optimizable.family
+            plottype $retcor.methods.section_retcor_peakgroups_non_optimizable.plottype
+        #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="True">
+            <conditional name="methods">
+                <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below. Only the density method is available so far">
+                    <option value="density" selected="true">density</option>
+                </param>
+                <when value="density">
+                    <section name="section_group_density_optiomizable"  title="Optimizable parameters" expanded="True">
+                        <conditional name="conditional_parameter">
+                            <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values">
+                                <option value="bw">Bandwidth [bw]</option>
+                                <option value="mzwid">Width of overlapping m/z slices [mzwid]</option>
+                            </param>
+                            <when value="bw">
+                                <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: 22,38)">
+                                    <validator type="regex" message="Should be this format XX,YY">[0-9]+,[0-9]+</validator>
+                                </param>
+                                <expand macro="group_density_mzwid_fixed" />
+                            </when>
+                            <when value="mzwid">
+                                <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: 0.015,0.035)" >
+                                    <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator>
+                                </param>
+                                <expand macro="group_density_bw_fixed" />
+                            </when>
+                        </conditional>
+                    </section>
+                    <section name="section_group_density_non_optimizable" title="Non optimizable parameters"  expanded="True">
+                        <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" />
+                        <param name="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />
+                    </section>
+                </when>
+            </conditional>
+        </section>
+
+        <section name="retcor" title="Retcor Options" expanded="True">
+            <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">
+                    <section name="section_retcor_obiwarp_non_optimizable" title="Non optimizable parameters"  expanded="True">
+                        <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)" />
+                    </section>
+                </when>
+                <when value="peakgroups">
+                    <section name="section_retcor_peakgroups_non_optimizable" title="Non optimizable parameters"  expanded="True">
+                        <param name="smooth" type="select" label="Smooth method" help="[smooth] only the 'loess’ for non-linear alignment is available so far" >
+                            <option value="loess">loess</option>
+                        </param>
+                        <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />
+                        <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" />
+                        <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>
+                        <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>
+                        <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>
+                    </section>
+                </when>
+            </conditional>
+
+        </section>
+
+        <expand macro="input_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"/>
+            <expand macro="test_file_load_zip"/>
+            <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup.tsv" />
+        </test>-->
+
+        <test>
+            <param name="image" value="faahKO.xset.RData"/>
+            <section name="group">
+                <conditional name="methods">
+                    <param name="method" value="density"/>
+                    <section name="section_group_density_optiomizable">
+                        <conditional name="conditional_parameter">
+                            <param name="bw" value="28,32"/>
+                            <param name="mzwid" value="0.25"/>
+                        </conditional>
+                    </section>
+                    <section name="section_group_density_non_optimizable">
+                        <param name="minfrac" value="1"/>
+                    </section>
+                </conditional>
+            </section>
+            <section name="retcor">
+                <conditional name="methods">
+                    <param name="method" value="peakgroups"/>
+                    <section name="section_retcor_peakgroups_non_optimizable">
+                        <param name="smooth" value="loess"/>
+                        <param name="rextra" value="1"/>
+                        <param name="missing" value="1"/>
+                    </section>
+                </conditional>
+            </section>
+            <expand macro="test_file_load_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"/>
+            <expand macro="test_file_load_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" />
+            <expand macro="test_file_load_single"/>
+            <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>