Mercurial > repos > workflow4metabolomics > xcms_refine
diff abims_xcms_refine.xml @ 0:eb115eb8f25c draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
| author | workflow4metabolomics |
|---|---|
| date | Thu, 17 Jun 2021 07:42:55 +0000 |
| parents | |
| children | 20f8ebc3a391 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_refine.xml Thu Jun 17 07:42:55 2021 +0000 @@ -0,0 +1,264 @@ +<tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="3.12.0+galaxy0"> + + <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.xset.merged.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.xset.merged.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.xset.merged.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>