Mercurial > repos > lecorguille > xcms_fillpeaks
view abims_xcms_fillPeaks.xml @ 27:ec9aebabc1d2 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
| author | workflow4metabolomics |
|---|---|
| date | Mon, 15 Jul 2024 15:58:27 +0000 |
| parents | bb9ee352fce0 |
| children |
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<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Integrate areas of missing peaks</description> <macros> <import>macros.xml</import> <import>macros_xcms.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ @COMMAND_RSCRIPT@/xcms_fillpeaks.r image '$image' ## Advanced expandMz $Adv.expandMz expandRt $Adv.expandRt ppm $Adv.ppm @COMMAND_PEAKLIST@ @COMMAND_FILE_LOAD@ @COMMAND_LOG_EXIT@ ]]></command> <inputs> <param name="image" type="data" format="rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from groupChromPeaks" /> <section name="Adv" title="Advanced Options" expanded="False"> <param argument="expandMz" type="integer" value="0" label="Value by which the mz width of peaks should be expanded" help="Each peak is expanded in mz direction by ‘expandMz *’ their original mz width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the mz width of the peak resulting in peakswith twice their original size in mz direction (expansion by half mz width to both sides)." /> <param argument="expandRt" type="integer" value="0" label="Value by which the RT width of peaks should be expanded" help="Each peak is expanded in RT direction by ‘expandRt *’ their original RT width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the RT width of the peak resulting in peakswith twice their original size in RT direction (expansion by half RT width to both sides)."/> <param argument="ppm" type="integer" value="0" label="Specifying a ppm by which the mz width of the peak region should be expanded" help="For peaks with an mz width smaller than ‘mean(c(mzmin, mzmax)) * ppm / 1e6’, the ‘mzmin’ will be replaced by ‘mean(c(mzmin, mzmax)) - (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’ and ‘mzmax’ by ‘mean(c(mzmin, mzmax)) + (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’. This is applied before eventually expanding the mz width using the ‘expandMz’ parameter." /> </section> <expand macro="input_peaklist_section"/> <expand macro="input_file_load"/> </inputs> <outputs> <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillChromPeaks.RData" from_work_dir="fillpeaks.RData" /> <expand macro="output_peaklist" function="fillpeaks" /> </outputs> <tests> <!--<test> <param name="image" value="xset.group.retcor.group.RData" ftype="rdata"/> <param name="method" value="chrom"/> <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> <assert_stdout> <has_text text="object with 4 samples" /> <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" /> <has_text text="Mass range: 50.0021-999.9863 m/z" /> <has_text text="Peaks: 199718 (about 49930 per sample)" /> <has_text text="Peak Groups: 48958" /> <has_text text="Sample classes: bio, blank" /> </assert_stdout> </test>--> <!-- Issue with fillpeaks because it seems that there are too many NA <test> <param name="image" value="faahKO.xset.group.retcor.group.RData" ftype="rdata"/> <param name="method" value="chrom"/> <conditional name="peaklist"> <param name="peaklistBool" value="true" /> <param name="convertRTMinute" value="false" /> <param name="numDigitsMZ" value="4" /> <param name="numDigitsRT" value="1" /> </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: 32720 (about 8180 per sample)" /> <has_text text="Peak Groups: 8209" /> <has_text text="Sample classes: KO, WT" /> </assert_stdout> <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" /> <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" /> </test> <test> <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData" ftype="rdata"/> <param name="method" value="chrom"/> <conditional name="peaklist"> <param name="peaklistBool" value="true" /> <param name="convertRTMinute" value="false" /> <param name="numDigitsMZ" value="4" /> <param name="numDigitsRT" value="1" /> </conditional> <expand macro="test_file_load_single"/> <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: 32720 (about 8180 per sample)" /> <has_text text="Peak Groups: 8209" /> <has_text text="Sample classes: KO, WT" /> </assert_stdout> <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" /> <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" /> </test>--> <!--<test> <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/> <conditional name="peaklist"> <param name="peaklistBool" value="true" /> <param name="convertRTMinute" value="false" /> <param name="numDigitsMZ" value="4" /> <param name="numDigitsRT" value="1" /> <param name="naTOzero" value="false" /> </conditional> <expand macro="test_file_load_single"/> <assert_stdout> <has_text text="expandMz: 0" /> <has_text text="expandRt: 0" /> <has_text text="object with 4 samples" /> <has_text text="Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes)" /> <has_text text="Mass range: 200.1-600 m/z" /> <has_text text="Peaks: 15230 (about 3808 per sample)" /> <has_text text="Peak Groups: 6332" /> <has_text text="Sample classes: KO, WT" /> </assert_stdout> <output name="variableMetadata" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv" /> <output name="dataMatrix" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.tsv" /> </test>--> <test expect_num_outputs="3"> <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.RData" ftype="rdata"/> <section name="peaklist"> <param name="peaklistBool" value="true" /> <param name="convertRTMinute" value="false" /> <param name="numDigitsMZ" value="4" /> <param name="numDigitsRT" value="1" /> </section> <expand macro="test_file_load_single"/> <assert_stdout> <has_text text="expandMz: 0" /> <has_text text="expandRt: 0" /> <has_text text="object with 4 samples" /> <has_text text="Time range: 2507.6-4481.8 seconds (41.8-74.7 minutes)" /> <has_text text="Mass range: 200.1-600 m/z" /> <has_text text="Peaks: 18995 (about 4749 per sample)" /> <has_text text="Peak Groups: 8209" /> <has_text text="Sample classes: KO, WT" /> </assert_stdout> <output name="variableMetadata" file="faahKO-single-class.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" /> <output name="dataMatrix" file="faahKO-single-class.xset.group.retcor.group.fillPeaks.dataMatrix.NAless.tsv" /> </test> </tests> <help><![CDATA[ @HELP_AUTHORS@ =================== xcms fillChromPeaks =================== ----------- Description ----------- **Integrate areas of missing peaks** For each sample, identify peak groups where that sample is not represented. For each of those peak groups, integrate the signal in the region of that peak group and create a new peak. ----------------- Workflow position ----------------- **Upstream tools** ========================= ============================ ================== Name Output file Format ========================= ============================ ================== xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group ========================= ============================ ================== **Downstream tools** =========================== =========================== ======================= Name Output file Format =========================== =========================== ======================= CAMERA.annotate ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks --------------------------- --------------------------- ----------------------- xcms.process_history ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks =========================== =========================== ======================= **General schema of the metabolomic workflow** .. image:: xcms_fillpeaks_workflow.png --------------------------------------------------- ---------- Parameters ---------- | See the fillChromPeaks_manual_ .. _fillChromPeaks_manual: https://rdrr.io/bioc/xcms/man/fillChromPeaks.html @HELP_XCMS_MANUAL@ @HELP_PEAKLIST@ ------------ Output files ------------ xset.fillPeaks.RData : rdata.xcms.fillpeaks format | Rdata file that will be used in the **CAMERA.annotate** or **xcms.process_history** step of the workflow. @HELP_PEAKLIST_OUTPUT@ --------------------------------------------------- Changelog/News -------------- @HELP_XCMS_NEWVERSION_31200@ @HELP_XCMS_NEWVERSION_3610@ @HELP_XCMS_NEWVERSION_3440@ - BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378 **Version 3.0.0.2 - 09/11/2018** - BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist **Version 3.0.0.1 - 09/10/2018** - IMPROVEMENT: the export of the PeakList is now mandatory **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. - UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW). xcms will detect from the data the peak picking method used in findChromPeaks - UPDATE: since xcms 3.0.0, new parameters are available: expandMz, expandRt and ppm **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 - 07/02/2017** - IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom) - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data **Version 2.0.8 - 22/12/2016** - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate **Version 2.0.7 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 **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 - 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>