changeset 27:8242376d9f35 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
author workflow4metabolomics
date Thu, 14 Mar 2024 15:35:44 +0000
parents 36480435e92b
children
files abims_xcms_refine.xml abims_xcms_retcor.xml xcms_refine.r xcms_retcor.r
diffstat 4 files changed, 490 insertions(+), 390 deletions(-) [+]
line wrap: on
line diff
--- a/abims_xcms_refine.xml	Mon Sep 11 09:21:15 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,264 +0,0 @@
-<tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-
-    <description>Remove or merge chromatographic peaks based on specific criteria.</description>
-
-    <macros>
-        <import>macros.xml</import>
-        <import>macros_xcms.xml</import>
-    </macros>
-
-    <expand macro="requirements"/>
-
-    <expand macro="stdio"/>
-
-    <command><![CDATA[
-        @COMMAND_RSCRIPT@/xcms_refine.r
-        image '$image'
-
-        method $methods.method
-        #if $methods.method == "CleanPeaks":
-            maxPeakwidth $methods.maxPeakwidth
-        #elif $methods.method == "FilterIntensity":
-            threshold $methods.threshold
-            nValues $methods.nValues
-            value $methods.value
-        #else:
-            expandRt $methods.expandRt
-            expandMz $methods.expandMz
-            ppm $methods.ppm
-            minProp $methods.minProp
-        #end if
-
-        msLevel $msLevel
-
-        @COMMAND_FILE_LOAD@
-
-        @COMMAND_LOG_EXIT@
-   ]]></command>
-
-    <inputs>
-        <param name="image" type="data" format="rdata.xcms.findchrompeaks" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks" />
-        <conditional name="methods">
-            <param name="method" type="select" label="Method for peak refinement" help="See the help section below">
-                <option value="CleanPeaks" selected="true">CleanPeaks - remove peaks that are too wide</option>
-                <option value="FilterIntensity">FilterIntensity - remove peaks with too low intensity</option>
-                <option value="MergeNeighboringPeaks">MergeNeighboringPeaks - combine peaks that are too close together</option>
-            </param>
-            <when value="CleanPeaks">
-                <param argument="maxPeakwidth" type="float" value="10" label="MaxPeakWidth" help="maximum peak width in seconds.  See CleanPeaks manual (linked in help below)." />
-            </when>
-            <when value="FilterIntensity">
-                <param argument="threshold" type="float" value="0" label="minimal required intensity" help="minimal required intensity for a peak to be retained.  Defaults to 0.0." />
-                <param argument="nValues" type="integer" value="1" label="minimum number of data points per peak" help="number of data points (per chromatographic peak) that have to be >= threshold. Defaults to 1." />
-                <param name="value" type="select" label="Definition of peak intensity" help="See the FilterIntensity manual (linked in help below). 'intb' requires centWave processed data">
-                    <option value="maxo" selected="true">maxo - use maximum peak intensities</option>
-                    <option value="into">into - use integrated peak intensities</option>
-                    <option value="intb">intb - use baseline-corrected integrated peak intensities</option>
-                </param>
-            </when>
-            <when value="MergeNeighboringPeaks">
-                <param argument="expandRt" type="float" value="2" label="rt expansion (seconds)" help="seconds of expansion of retention time window (on both sides) to check for overlapping peaks. Defaults to 2." />
-                <param argument="expandMz" type="float" value="0" label="m/z expansion (m/z units)" help="'m/z units' of expansion of m/z window (on both sides) to check for overlapping peaks. Defaults to 0." />
-                <param argument="ppm" type="float" value="10" label="ppm expansion (ppm units)" help="'relative 'm/z units' (in parts per million) of expansion of m/z window (on both sides) to check for overlapping peaks. Defaults to 10." />
-                <param argument="minProp" type="float" value="0.75" label="minimum proportion at midpoint" help="See MergeNeighboringPeaks manual (linked in help below).  Minimum proportion midway between peaks relative to the smaller peak's 'maxo' (maximal intensity at peak apex).  Defaults to 0.75." />
-            </when>
-        </conditional>
-        <param argument="msLevel" type="integer" value="1" label="msLevel for refinement" help="the MS level on which refinement should be performed. Defaults to 1." />
-
-        <expand macro="input_file_load"/>
-    </inputs>
-
-    <outputs>
-        <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.refine.RData" from_work_dir="xcmsSet.RData" />
-    </outputs>
-
-    <tests>
-        <!--
-            test 1 - MergeNeighboringPeaks method
-        -->
-        <test>
-            <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
-            <conditional name="methods">
-                <param name="method" value="MergeNeighboringPeaks"/>
-                <param name="expandRt" value="2" />
-                <param name="expandMz" value="0" />
-                <param name="ppm" value="10" />
-                <param name="minProp" value="0.75" />
-            </conditional>
-            <expand macro="test_file_load_single"/>
-            <assert_stderr>
-                <has_text text="Evaluating 547 peaks in file wt15.CDF for merging ... OK" />
-                <has_text text="Evaluating 547 peaks in file wt16.CDF for merging ... OK" />
-                <has_text text="Evaluating 558 peaks in file ko15.CDF for merging ... OK"/>
-                <has_text text="Evaluating 589 peaks in file ko16.CDF for merging ... OK" />
-                <has_text text="Merging reduced 9251 chromPeaks to 9093" />
-            </assert_stderr>
-            <assert_stdout>
-                <has_text text="object with 4 samples" />
-                <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
-                <has_text text="Mass range: 200.1-600 m/z" />
-                <has_text text="Peaks: 9093 (about 2273 per sample)" />
-            </assert_stdout>
-        </test>
-        <!--
-            test 2 - FilterIntensity method
-        -->
-        <test>
-            <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
-            <conditional name="methods">
-                <param name="method" value="FilterIntensity"/>
-                <param name="threshold" value="1e5" />
-                <param name="nValues" value="3" />
-                <param name="value" value="into" />
-            </conditional>
-            <expand macro="test_file_load_single"/>
-            <assert_stderr>
-                <has_text text="Removed 9018 chromatographic peaks" />
-            </assert_stderr>
-            <assert_stdout>
-                <has_text text="object with 4 samples" />
-                <has_text text="Time range: 2657.9-4124.2 seconds (44.3-68.7 minutes)" />
-                <has_text text="Mass range: 256.1-599.4 m/z" />
-                <has_text text="Peaks: 233 (about 58 per sample)" />
-            </assert_stdout>
-        </test>
-        <!--
-            test 3 - CleanPeaks method
-        -->
-        <test>
-            <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
-            <conditional name="methods">
-                <param name="method" value="CleanPeaks"/>
-                <param name="maxPeakwidth" value="8" />
-            </conditional>
-            <expand macro="test_file_load_single"/>
-            <assert_stderr>
-                <has_text text="Removed 6037 of 9251 chromatographic peaks" />
-            </assert_stderr>
-            <assert_stdout>
-                <has_text text="object with 4 samples" />
-                <has_text text="Time range: 2524.9-4473.2 seconds (42.1-74.6 minutes)" />
-                <has_text text="Mass range: 200.2-600 m/z" />
-                <has_text text="Peaks: 3214 (about 804 per sample)" />
-            </assert_stdout>
-        </test>
-    </tests>
-
-    <help><![CDATA[
-
-.. class:: infomark
-
-**Authors**  Johannes Rainer Johannes.Rainer@eurac.edu and Mar Garcia-Aloy mar.garcia@fmach.it
-
-@HELP_AUTHORS_WRAPPERS@
-
----------------------------------------------------
-
-
-=====================
-xcms refineChromPeaks
-=====================
-
------------
-Description
------------
-
-After peak identification with xcms findChromPeaks (xcmsSet), this tool refines those peaks.
-It either removes peaks that are too wide or removes peaks with too low intensity or combines peaks that are too close together.
-
-Note well that refineChromPeaks methods will always remove feature definitions,
-because a call to this method can change or remove identified chromatographic peaks, which may be part of features.
-Therefore it must only be run immediately after findChromPeaks (xcmsSet).
-
------------------
-Workflow position
------------------
-
-**Upstream tools**
-
-==================================== ======================== ==============================
-Name                                 Output file              Format
-==================================== ======================== ==============================
-xcms.findChromPeaks Merger (single)  xset.merged.RData        rdata.xcms.findchrompeaks
------------------------------------- ------------------------ ------------------------------
-xcms.findChromPeaks (zip)            ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
-==================================== ======================== ==============================
-
-
-**Downstream tools**
-
-==================================== ======================== =========================
-Name                                 Output file              Format
-==================================== ======================== =========================
-xcms.findChromPeaks Merger (single)  ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
------------------------------------- ------------------------ -------------------------
-xcms.groupChromPeaks (zip)           ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
-==================================== ======================== =========================
-
-**General schema of the metabolomic workflow**
-
-This tool would appear between findChromPeaks and group, but only when the choice of peaks needs to be refined, e.g., to accommodate HILIC data.
-
----------------------------------------------------
-
-----------
-Parameters
-----------
-
-Method to use for refinement
-----------------------------
-
-**CleanPeaks**
-
-    | Remove chromatographic peaks with too large rt width.
-    | See the CleanPeaks_manual_
-
-**FilterIntensity**
-
-    | Remove chromatographic peaks based on intensity.
-    | See the FilterIntensity_manual_
-
-**MergeNeighboringPeaks**
-
-    | Merge neighboring and overlapping chromatographic peaks.
-    | See the MergeNeighboringPeaks_manual_
-
-.. _CleanPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-clean.html
-.. _FilterIntensity_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-filter-intensity.html
-.. _MergeNeighboringPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-merge.html
-
-@HELP_XCMS_MANUAL@
-
-------------
-Output files
-------------
-
-xset.RData: rdata.xcms.findchrompeaks format
-
-    | (single) RData files that are necessary in the second step of the workflow "xcms.groupChromPeaks" - must be merged first using "xcms.findChromPeaks Merger"
-    | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".
-
-
----------------------------------------------------
-
-Changelog/News
---------------
-
-.. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
-
-
-**Version 3.6.1.0 - 08/02/2021**
-
-- NEW: first version of tool wrapper
-
-
-    ]]></help>
-
-    <citations>
-      <citation type="doi">10.5281/zenodo.3909299</citation>
-      <expand macro="citation_w4m"/>
-      <citation type="doi">10.1021/ac051437y</citation>
-    </citations>
-
-
-</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_xcms_retcor.xml	Thu Mar 14 15:35:44 2024 +0000
@@ -0,0 +1,383 @@
+<tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+
+    <description>Retention Time Correction</description>
+
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_xcms.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command><![CDATA[
+        @COMMAND_RSCRIPT@/xcms_retcor.r
+        image '$image'
+
+        method $methods.method
+        #if $methods.method == "PeakGroups":
+            minFraction $methods.minFraction
+            extraPeaks $methods.extraPeaks
+            smooth $methods.smooth_cond.smooth
+            ## PeakGroupsSmoothLoess Advanced
+            span $methods.smooth_cond.PeakGroupsSmoothLoessAdv.span
+            family $methods.smooth_cond.PeakGroupsSmoothLoessAdv.family
+        #else
+            binSize $methods.binSize
+            ## Advanced
+            #if $methods.ObiwarpAdv.centerSample != "":
+                centerSample $methods.ObiwarpAdv.centerSample
+            #end if
+            response $methods.ObiwarpAdv.response
+            distFun $methods.ObiwarpAdv.distFunCond.distFun
+            gapInit $methods.ObiwarpAdv.distFunCond.gapInit
+            gapExtend $methods.ObiwarpAdv.distFunCond.gapExtend
+            factorDiag $methods.ObiwarpAdv.factorDiag
+            factorGap $methods.ObiwarpAdv.factorGap
+            localAlignment $methods.ObiwarpAdv.localAlignmentCond.localAlignment
+            initPenalty $methods.ObiwarpAdv.localAlignmentCond.initPenalty
+        #end if
+
+        @COMMAND_FILE_LOAD@
+
+        @COMMAND_LOG_EXIT@
+    ]]></command>
+
+    <inputs>
+        <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks" />
+        <conditional name="methods">
+            <param name="method" type="select" label="Method to use for retention time correction" help="See the help section below" >
+                <option value="PeakGroups" selected="true">PeakGroups - retention time correction based on aligment of features (peak groups) present in most/all samples.</option>
+                <option value="Obiwarp">Obiwarp - alignment based on the complete mz-rt data.</option>
+            </param>
+            <when value="PeakGroups">
+                <param argument="minFraction" type="float" value="0.9" min="0" max="1" label="Minimum required fraction of samples in which peaks for the peak group were identified" help="(previously missing)"/>
+                <param argument="extraPeaks" type="integer" value="1" label="Maximal number of additional peaks for all samples to be assigned to a peak group for retention time correction"  help="For a data set with 6 samples, ‘extraPeaks = 1’ uses all peak groups with a total peak count lower or equal to ‘6 + 1’. The total peak count is the total number of peaks being assigned to a peak group and considers also multiple peaks within a sample being assigned to the group. (previously extra)" />
+                <conditional name="smooth_cond">
+                    <param argument="smooth" type="select" label="Smooth method" >
+                        <option value="loess" selected="true">loess - non-linear alignment</option>
+                        <option value="linear">linear - linear alignment</option>
+                    </param>
+                    <when value="loess">
+                        <section name="PeakGroupsSmoothLoessAdv" title="Advanced Options" expanded="False">
+                            <param argument="span" type="float" value="0.2" label="Degree of smoothing for the loess fitting" />
+                            <param argument="family" type="select" label="Family" help="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>
+                        </section>
+                    </when>
+                    <when value="linear" />
+                </conditional>
+            </when>
+            <when value="Obiwarp">
+                <param argument="binSize" type="float" value="1" label="Bin size (in mz dimension) to be used for the profile matrix generation" help="See ‘step’ parameter in ‘profile-matrix’ documentation for more details. (previously profStep)" />
+                <section name="ObiwarpAdv" title="Advanced Options" expanded="False">
+                    <param argument="centerSample" type="integer" value="" optional="true" label="Index of the center sample in the experiment" help="It defaults to ‘floor(median(1:length(fileNames(object))))’" />
+                    <param argument="response" type="integer" value="1" label="Defining the responsiveness of warping" help="with ‘response = 0’ giving linear warping on start and end points and ‘response = 100’ warping using all bijective anchors." />
+                    <conditional name="distFunCond">
+                        <param argument="distFun" type="select" label="Distance function to be used">
+                            <option value="cor_opt" selected="true">cor_opt - calculate only 10% diagonal band of distance matrix; better runtime</option>
+                            <option value="cor">cor - Pearson's correlation</option>
+                            <option value="cov">cov - covariance</option>
+                            <option value="prd">prd - product</option>
+                            <option value="euc">euc - Euclidian distance</option>
+                        </param>
+                        <when value="cor_opt">
+                            <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" />
+                            <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" />
+                        </when>
+                        <when value="cor">
+                            <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" />
+                            <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" />
+                        </when>
+                        <when value="cov">
+                            <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" />
+                            <param argument="gapExtend" type="float" value="11.7" label="Penalty for gap enlargement" />
+                        </when>
+                        <when value="prd">
+                            <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" />
+                            <param argument="gapExtend" type="float" value="7.8" label="Penalty for gap enlargement" />
+                        </when>
+                        <when value="euc">
+                            <param argument="gapInit" type="float" value="0.9" label="Penalty for gap opening" />
+                            <param argument="gapExtend" type="float" value="1.8" label="Penalty for gap enlargement" />
+                        </when>
+                    </conditional>
+                    <param argument="factorDiag" type="float" value="2" label="Local weight applied to diagonal moves in the alignment" />
+                    <param argument="factorGap" type="float" value="1" label="local weight for gap moves in the alignment" />
+                    <conditional name="localAlignmentCond">
+                        <param argument="localAlignment" type="select" label="Whether a local alignment should be performed instead of the default global alignment">
+                            <option value="FALSE" selected="true">FALSE</option>
+                            <option value="TRUE">TRUE</option>
+                        </param>
+                        <when value="FALSE">
+                            <param argument="initPenalty" type="hidden" value="0" label="Penalty for initiating an alignment" />
+                        </when>
+                        <when value="TRUE">
+                            <param argument="initPenalty" type="float" value="0"  label="Penalty for initiating an alignment" />
+                        </when>
+                    </conditional>
+                </section>
+            </when>
+        </conditional>
+
+        <expand macro="input_file_load"/>
+
+    </inputs>
+
+    <outputs>
+        <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.adjustRtime.RData" from_work_dir="retcor.RData" />
+        <data name="rawVSadjustedPdf" format="pdf"  label="${image.name[:-6]}_rawVSadjusted.adjustRtime.Rplots.pdf" from_work_dir="raw_vs_adjusted_rt.pdf" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
+            <conditional name="methods">
+                <param name="method" value="PeakGroups"/>
+                <param name="extraPeaks" value="1"/>
+                <param name="minFraction" value="1"/>
+                <conditional name="smooth_cond">
+                    <param name="smooth" value="loess"/>
+                    <section name="PeakGroupsSmoothLoessAdv">
+                        <param name="span" value="0.2"/>
+                        <param name="family" value="gaussian"/>
+                    </section>
+                </conditional>
+            </conditional>
+            <expand macro="test_file_load_single"/>
+            <assert_stdout>
+                <has_text text="extraPeaks: 1" />
+                <has_text text="minFraction: 1" />
+                <has_text text="span: 0.2" />
+                <has_text text="object with 4 samples" />
+                <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
+                <has_text text="Mass range: 200.1-600 m/z" />
+                <has_text text="Peaks: 9251 (about 2313 per sample)" />
+                <has_text text="Peak Groups: 0" />
+                <has_text text="Sample classes: KO, WT" />
+            </assert_stdout>
+        </test>
+        <!-- DISABLE FOR TRAVIS : Zip
+        <test>
+            <param name="image" value="faahKO.xset.group.RData" ftype="rdata"/>
+            <conditional name="methods">
+                <param name="method" value="PeakGroups"/>
+                <param name="extraPeaks" value="1"/>
+                <param name="minFraction" value="1"/>
+                <conditional name="smooth_cond">
+                    <param name="smooth" value="loess"/>
+                    <section name="PeakGroupsSmoothLoessAdv">
+                        <param name="span" value="0.2"/>
+                        <param name="family" value="gaussian"/>
+                    </section>
+                </conditional>
+            </conditional>
+            <expand macro="test_file_load_zip"/>
+            <assert_stdout>
+                <has_text text="object with 4 samples" />
+                <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
+                <has_text text="Mass range: 200.1-600 m/z" />
+                <has_text text="Peaks: 9251 (about 2313 per sample)" />
+                <has_text text="Peak Groups: 0" />
+                <has_text text="Sample classes: KO, WT" />
+            </assert_stdout>
+        </test>
+        -->
+        <!-- DISABLE FOR TRAVIS
+        Test to test the different methods parameters
+        <test>
+            <param name="image" value="faahKO-single-class.xset.group.RData" ftype="rdata"/>
+            <conditional name="methods">
+                <param name="method" value="Obiwarp"/>
+                <section name="ObiwarpAdv">
+                    <param name="centerSample" value="1"/>
+                    <param name="response" value="0"/>
+                    <conditional name="distFunCond">
+                        <param name="distFun" value="cov"/>
+                        <param name="gapInit" value="0.1" />
+                    </conditional>
+                </section>
+            </conditional>
+            <expand macro="test_file_load_single"/>
+            <assert_stdout>
+                <has_text text="centerSample: 1" />
+                <has_text text="response: 0" />
+                <has_text text="distFun: cov" />
+                <has_text text="gapInit: 0.1" />
+                <has_text text="gapExtend: 11.7" />
+            </assert_stdout>
+        </test>
+        -->
+    </tests>
+
+    <help><![CDATA[
+
+@HELP_AUTHORS@
+
+================
+xcms adjustRtime
+================
+
+-----------
+Description
+-----------
+
+After matching peaks into groups, xcms can use those groups to identify and correct
+correlated drifts in retention time from run to run. The aligned peaks can then be
+used for a second pass of peak grouping which will be more accurate than the first.
+The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful
+for identifying retention time drifts. Some groups may be missing peaks from a large
+fraction of samples and thus provide an incomplete picture of the drift at that time point.
+Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.
+
+.. class:: warningmark
+
+**After an adjustRtime step, it is mandatory to do a groupChromPeaks step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is
+discarded)**
+
+
+
+-----------------
+Workflow position
+-----------------
+
+
+**Upstream tools**
+
+========================= ============================ ==============================
+Name                      Output file                  Format
+========================= ============================ ==============================
+xcms.findChromPeaks       raw.xset.RData               rdata.xcms.findchrompeaks
+------------------------- ---------------------------- ------------------------------
+xcms.groupChromPeaks      ``*``.groupChromPeaks.RData  rdata.xcms.group
+========================= ============================ ==============================
+
+
+**Downstream tools**
+
+=========================== ============================ ================
+Name                        Output file                  Format
+=========================== ============================ ================
+xcms.groupChromPeaks        ``*``.groupChromPeaks.RData  rdata.xcms.group
+=========================== ============================ ================
+
+
+**General schema of the metabolomic workflow**
+
+.. image:: xcms_retcor_workflow.png
+
+---------------------------------------------------
+
+----------
+Parameters
+----------
+
+Method
+------
+
+**PeakGroups**
+
+    | This method performs retention time adjustment based on the alignment of chromatographic peak groups present in all/most samples (hence corresponding to house keeping compounds). First the retention time deviation of these peak groups is described by fitting either a polynomial (‘smooth = "loess"’) or a linear ( ‘smooth = "linear"’) model to the data points. These models are subsequently used to adjust the retention time of each spectrum in each sample.
+    | See the PeakGroups_manual_
+
+**Obiwarp**
+
+    | This method performs retention time adjustment using the Obiwarp method [Prince 2006]. It is based on the code at http://obi-warp.sourceforge.net but supports alignment of multiple samples by aligning each against a _center_ sample. The alignment is performed directly on the ‘profile-matrix’ and can hence be performed independently of the peak detection or peak grouping.
+    | See the Obiwarp_manual_
+
+.. _PeakGroups_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-peakGroups.html#heading-2
+.. _Obiwarp_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-obiwarp.html
+
+WARNING: if a retention time ajustment have already been applied to your data.
+The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments.
+
+@HELP_XCMS_MANUAL@
+
+------------
+Output files
+------------
+
+xset.groupChromPeaks.adjustRtime.RData: rdata.xcms.retcor format
+
+    | Rdata file that will be necessary in the **xcms.groupChromPeaks** step of the workflow.
+
+
+---------------------------------------------------
+
+Changelog/News
+--------------
+
+@HELP_XCMS_NEWVERSION_31200@
+
+**Version 3.6.1+galaxy1 - 13/02/2020**
+
+- NEW: if a retention time ajustment have already been applied to your data. The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments.
+
+@HELP_XCMS_NEWVERSION_3610@
+
+**Version 3.4.4.1 - 30/04/2019**
+
+- BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
+
+@HELP_XCMS_NEWVERSION_3440@
+
+**Version 3.0.0.0 - 08/03/2018**
+
+- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
+
+- NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty)
+
+- IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
+
+- CHANGE: removing of the TIC and BPC plots. You can now use the dedicated tool "xcms plot chromatogram"
+
+
+**Version 2.1.1 - 29/11/2017**
+
+- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
+
+
+**Version 2.1.0 - 03/02/2017**
+
+- IMPROVEMENT: xcms.retcor can deal with merged individual data
+
+
+**Version 2.0.8 - 22/12/2016**
+
+- BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
+
+
+@HELP_XCMS_NEWVERSION_2090@
+
+
+**Version 2.0.6 - 04/04/2016**
+
+- TEST: refactoring to pass planemo test using conda dependencies
+
+
+**Version 2.0.5 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- BUGFIX: some pdf remained empty even when the process succeed
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+- UPDATE: refactoring to feed the new report tool
+
+
+**Version 2.0.2 - 02/06/2015**
+
+- 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>
+
+
+    <expand macro="citation" />
+
+</tool>
--- a/xcms_refine.r	Mon Sep 11 09:21:15 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-#!/usr/bin/env Rscript
-
-# ----- LOG FILE -----
-log_file <- file("log.txt", open  =  "wt")
-sink(log_file)
-sink(log_file, type = "output")
-
-
-# ----- PACKAGE -----
-cat("\tSESSION INFO\n")
-
-#Import the different functions
-source_local <- function(fname) {
-  argv <- commandArgs(trailingOnly = FALSE)
-  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
-  source(paste(base_dir, fname, sep = "/"))
-}
-source_local("lib.r")
-
-pkgs <- c("xcms", "batch", "RColorBrewer")
-loadAndDisplayPackages(pkgs)
-cat("\n\n")
-
-# ----- ARGUMENTS -----
-cat("\tARGUMENTS INFO\n")
-# interpretation of arguments given in command line as an R list of objects
-args <- parseCommandArgs(evaluate = FALSE)
-write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
-
-cat("\n\n")
-
-# ----- PROCESSING INFILE -----
-cat("\tARGUMENTS PROCESSING INFO\n")
-
-#saving the specific parameters
-args_method  <- args$method
-args_image   <- args$image
-args_msLevel <- args$msLevel
-param_args <- list()
-
-if (args_method == "CleanPeaks") {
-  param_args$maxPeakwidth <- args$maxPeakwidth
-} else if (args_method == "FilterIntensity") {
-  param_args$threshold <- args$threshold
-  param_args$value <- args$value
-  param_args$nValues <- args$nValues
-} else if (args_method == "MergeNeighboringPeaks") {
-  param_args$expandRt <- args$expandRt
-  param_args$expandMz <- args$expandMz
-  param_args$ppm      <- args$ppm
-  param_args$minProp  <- args$minProp
-}
-
-cat("\n\n")
-
-
-# ----- ARGUMENTS PROCESSING -----
-cat("\tINFILE PROCESSING INFO\n")
-
-#image is an .RData file necessary to use xset variable given by previous tools
-load(args_image)
-if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*")
-
-# Handle infiles
-if (!exists("singlefile")) singlefile <- NULL
-if (!exists("zipfile")) zipfile <- NULL
-rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
-zipfile <- rawFilePath$zipfile
-singlefile <- rawFilePath$singlefile
-
-cat("\n\n")
-
-
-# ----- MAIN PROCESSING INFO -----
-cat("\tMAIN PROCESSING INFO\n")
-
-
-cat("\t\tPREPARE PARAMETERS\n\n")
-
-if (args_method == "CleanPeaks") {
-  refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth)
-} else if (args_method == "FilterIntensity") {
-  refineChromPeaksParam <- FilterIntensityParam(
-    threshold = param_args$threshold,
-    nValues = param_args$nValues,
-    value = param_args$value
-  )
-} else if (args_method == "MergeNeighboringPeaks") {
-  refineChromPeaksParam <- MergeNeighboringPeaksParam(
-    expandRt = param_args$expandRt,
-    expandMz = param_args$expandMz,
-    ppm = param_args$ppm,
-    minProp = param_args$minProp
-  )
-}
-
-cat(str(refineChromPeaksParam))
-
-cat("\n\n\t\tCOMPUTE\n")
-
-xdata <- updateObject(xdata)
-
-xdata <- refineChromPeaks(xdata, param = refineChromPeaksParam)
-
-cat("\n\n")
-
-# ----- EXPORT -----
-
-cat("\tXCMSnExp OBJECT INFO\n")
-print(xdata)
-cat("\n\n")
-
-cat("\txcmsSet OBJECT INFO\n")
-# Get the legacy xcmsSet object
-xset <- getxcmsSetObject(xdata)
-print(xset)
-cat("\n\n")
-
-#saving R data in .Rdata file to save the variables used in the present tool
-objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
-save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData")
-
-cat("\n\n")
-
-
-cat("\tDONE\n")
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_retcor.r	Thu Mar 14 15:35:44 2024 +0000
@@ -0,0 +1,107 @@
+#!/usr/bin/env Rscript
+
+# ----- LOG FILE -----
+log_file <- file("log.txt", open = "wt")
+sink(log_file)
+sink(log_file, type = "output")
+
+
+# ----- PACKAGE -----
+cat("\tSESSION INFO\n")
+
+#Import the different functions
+source_local <- function(fname) {
+  argv <- commandArgs(trailingOnly = FALSE)
+  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  source(paste(base_dir, fname, sep = "/"))
+}
+source_local("lib.r")
+
+pkgs <- c("xcms", "batch", "RColorBrewer")
+loadAndDisplayPackages(pkgs)
+cat("\n\n")
+
+
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n")
+args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
+write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
+
+cat("\n\n")
+
+# ----- PROCESSING INFILE -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+#saving the specific parameters
+method <- args$method
+
+cat("\n\n")
+
+
+# ----- ARGUMENTS PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+load(args$image)
+args$image <- NULL
+if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
+
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+if (!exists("zipfile")) zipfile <- NULL
+rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+
+cat("\n\n")
+
+
+# ----- MAIN PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+
+cat("\t\tCOMPUTE\n")
+
+cat("\t\t\tAlignment/Retention Time correction\n")
+# clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
+args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))]
+
+adjustRtimeParam <- do.call(paste0(method, "Param"), args)
+print(adjustRtimeParam)
+
+if (hasAdjustedRtime(xdata)) {
+  cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment")
+  cat("Replace raw retention times with adjusted retention times.\n")
+  xdata <- applyAdjustedRtime(xdata)
+}
+xdata <- adjustRtime(xdata, param = adjustRtimeParam)
+
+cat("\n\n")
+
+
+# -- TIC --
+cat("\t\tDRAW GRAPHICS\n")
+getPlotAdjustedRtime(xdata)
+
+cat("\n\n")
+
+# ----- EXPORT -----
+
+cat("\tXCMSnExp OBJECT INFO\n")
+print(xdata)
+cat("\n\n")
+
+cat("\txcmsSet OBJECT INFO\n")
+# Get the legacy xcmsSet object
+xset <- getxcmsSetObject(xdata)
+print(xset)
+cat("\n\n")
+
+#saving R data in .Rdata file to save the variables used in the present tool
+objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
+save(list = objects2save[objects2save %in% ls()], file = "retcor.RData")
+
+cat("\n\n")
+
+
+cat("\tDONE\n")