Mercurial > repos > lecorguille > xcms_xcmsset
diff abims_xcms_xcmsSet.xml @ 29:5dba1c94fb94 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
| author | lecorguille |
|---|---|
| date | Tue, 24 Oct 2017 11:46:21 -0400 |
| parents | b90e4f92e8b5 |
| children | d71827ecd22c |
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--- a/abims_xcms_xcmsSet.xml Mon Apr 03 07:50:18 2017 -0400 +++ b/abims_xcms_xcmsSet.xml Tue Oct 24 11:46:21 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.0"> +<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.2.0"> <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description> <macros> @@ -21,9 +21,6 @@ xsetRdataOutput '$xsetRData' sampleMetadataOutput '$sampleMetadata' - ticspdf '$ticsRawPdf' - bicspdf '$bpcsRawPdf' - #if $options_scanrange.option == "show": scanrange "c($options_scanrange.scanrange)" @@ -59,7 +56,13 @@ scales "c($methods.scales)" SNR.method "$methods.SNR_method" #end if - @COMMAND_LOG_EXIT@ + + #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"): + && mv *-TIC_mqc.out $ticsRawTab + && mv *-BPC_mqc.out $bpcsRawTab + #end if + + @COMMAND_LOG_EXIT@; ]]></command> <inputs> @@ -155,39 +158,47 @@ <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." /> </when> </conditional> + + + <expand macro="input_tic_bpc_pdf"/> </inputs> <outputs> <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" /> + <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" /> + + <!-- SINGLE MODE --> + <data name="ticsRawTab" format="tabular" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.tabular"> + <filter>input.extension in ["mzxml","mzml","mzdata","netcdf"]</filter> + </data> + <data name="bpcsRawTab" format="tabular" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.tabular"> + <filter>input.extension in ["mzxml","mzml","mzdata","netcdf"]</filter> + </data> + + <!-- ZIP MODE --> <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv"> <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> </data> - <data name="ticsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" /> - <data name="bpcsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" /> - <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" /> + <data name="ticsRawPdf" format="pdf" from_work_dir="TICs.pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf"> + <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> + <filter>tic_bpc_pdf</filter> + </data> + <data name="bpcsRawPdf" format="pdf" from_work_dir="BPCs.pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf"> + <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> + <filter>tic_bpc_pdf</filter> + </data> + <collection name="ticsRawTabCollection" type="list" label="TIC raw tabular"> + <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> + <discover_datasets pattern="(?P<designation>.+)-TIC_mqc\.out" ext="tabular" visible="true" /> + </collection> + <collection name="bpcsRawTabCollection" type="list" label="BPC raw tabular"> + <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> + <discover_datasets pattern="(?P<designation>.+)-BPC_mqc\.out" ext="tabular" visible="true" /> + </collection> </outputs> <tests> - <!--<test> - <param name="input" value="sacuri_dir_root.zip" ftype="zip" /> - <param name="methods|method" value="matchedFilter" /> - <param name="methods|step" value="0.01" /> - <param name="methods|fwhm" value="4" /> - <param name="methods|options_m|option" value="show" /> - <param name="methods|options_m|max" value="50" /> - <param name="methods|options_m|snthresh" value="1" /> - <param name="methods|options_m|steps" value="2" /> - <output name="log"> - <assert_contents> - <has_text text="object with 4 samples" /> - <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" /> - <has_text text="Mass range: 50.0021-999.9863 m/z" /> - <has_text text="Peaks: 59359 (about 14840 per sample)" /> - <has_text text="Peak Groups: 0" /> - <has_text text="Sample classes: bio, blank" /> - </assert_contents> - </output> - </test> + <!-- <test> <param name="input" value="sacuri_current_root.zip" ftype="zip" /> <param name="methods|method" value="centWave" /> @@ -219,56 +230,21 @@ <has_text text="Sample classes: KO, WT" /> </assert_contents> </output> + <output_collection name="ticsRawTabCollection" type="list"> + <element name="ko15" value="ko15-TIC_mqc.out" /> + <element name="ko16" value="ko16-TIC_mqc.out" /> + <element name="wt15" value="wt15-TIC_mqc.out" /> + <element name="wt16" value="wt16-TIC_mqc.out" /> + </output_collection> + <output_collection name="bpcsRawTabCollection" type="list"> + <element name="ko15" value="ko15-BPC_mqc.out" /> + <element name="ko16" value="ko16-BPC_mqc.out" /> + <element name="wt15" value="wt15-BPC_mqc.out" /> + <element name="wt16" value="wt16-BPC_mqc.out" /> + </output_collection> </test> <!-- Passed but disable to save time for Travis" --> - <!--<test> - <param name="input" value="ko15.CDF" ftype="netcdf" /> - <param name="methods|method" value="centWave" /> - <param name="methods|ppm" value="25" /> - <param name="methods|peakwidth" value="20,50" /> - <output name="log"> - <assert_contents> - <has_text text="object with 1 samples" /> - <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" /> - <has_text text="Mass range: 200.2-600 m/z" /> - <has_text text="Peaks: 2262 (about 2262 per sample)" /> - <has_text text="Peak Groups: 0" /> - <has_text text="Sample classes: ." /> - </assert_contents> - </output> - </test> - <test> - <param name="input" value="ko16.CDF" ftype="netcdf" /> - <param name="methods|method" value="centWave" /> - <param name="methods|ppm" value="25" /> - <param name="methods|peakwidth" value="20,50" /> - <output name="log"> - <assert_contents> - <has_text text="object with 1 samples" /> - <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" /> - <has_text text="Mass range: 200.1-600 m/z" /> - <has_text text="Peaks: 2408 (about 2408 per sample)" /> - <has_text text="Peak Groups: 0" /> - <has_text text="Sample classes: ." /> - </assert_contents> - </output> - </test> - <test> - <param name="input" value="wt15.CDF" ftype="netcdf" /> - <param name="methods|method" value="centWave" /> - <param name="methods|ppm" value="25" /> - <param name="methods|peakwidth" value="20,50" /> - <output name="log"> - <assert_contents> - <has_text text="object with 1 samples" /> - <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" /> - <has_text text="Mass range: 200.2-599.8 m/z" /> - <has_text text="Peaks: 2278 (about 2278 per sample)" /> - <has_text text="Peak Groups: 0" /> - <has_text text="Sample classes: ." /> - </assert_contents> - </output> - </test> + <!-- <test> <param name="inputs|input" value="single_file" /> <param name="inputs|single_file" value="wt16.CDF" ftype="netcdf" /> @@ -301,6 +277,8 @@ <has_text text="Sample classes: ." /> </assert_contents> </output> + <output name="ticsRawTab" value="HU_neg_017-TIC_mqc.out" /> + <output name="bpcsRawTab" value="HU_neg_017-BPC_mqc.out" /> </test> <test> <param name="input" value="MM14.mzML" ftype="mzxml" /> @@ -317,6 +295,8 @@ <has_text text="Sample classes: ." /> </assert_contents> </output> + <output name="ticsRawTab" value="MM14-TIC_mqc.out" /> + <output name="bpcsRawTab" value="MM14-BPC_mqc.out" /> </test> </tests> @@ -328,7 +308,6 @@ Xcms.xcmsSet ============ ------------ Description ----------- @@ -338,18 +317,16 @@ .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf ------------------ Workflow position ----------------- **Upstream tools** -========================= ================= ======= ========= -Name output file format parameter -========================= ================= ======= ========= -NA NA zip NA -========================= ================= ======= ========= - ++------------------------+--------------------+-----------------------------+-----------+ +| Name | output file | format | parameter | ++------------------------+--------------------+-----------------------------+-----------+ +| Upload File | Dataset Collection | mzXML, mzML, mzData, netCDF | NA | ++------------------------+--------------------+-----------------------------+-----------+ **Downstream tools** @@ -358,90 +335,89 @@ +===========================+====================+=================+ |xcms.group | xset.RData | rdata.xcms.raw | +---------------------------+--------------------+-----------------+ -|PCA ellipsoid by factors | sampleMetadata.tsv | Tabular | -+---------------------------+--------------------+-----------------+ -|Anova | sampleMetadata.tsv | Tabular | -+---------------------------+--------------------+-----------------+ **Example of a metabolomic workflow** .. image:: xcms_xcmsset_workflow.png - ------- - -.. class:: infomark - -The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool. - --------------------------------------------------- - - ----------- Input files ----------- +Choose your inputs +------------------ + +---------------------------+----------------------------------+ -| Parameter : num + label | Format | +| Parameter | Format | +===========================+==================================+ +| OR : Single file | mzXML, mzML, mzData, netCDF | ++---------------------------+----------------------------------+ | OR : Zip file | zip | +---------------------------+----------------------------------+ -| OR : Single file | mzXML, mzML, mzData, netCDF | -+---------------------------+----------------------------------+ - -**Choose your inputs** You have two methods for your inputs: - | Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group" - | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). +* Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group" + +* Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). + +Single file +----------- + +This method is recommended because: + +* Since files are uploaded indivudially, they are smaller. And so they should be able to be uploaded using the Get Data tools. -Zip file: Steps for creating the zip file ------------------------------------------ +* It allow you to launch your xcmsSet in parallele. + +You just have to create a Dataset Collection as explain in this video_ + +.. _video: http://download.workflow4metabolomics.org/docs/170510_galaxy_xcms_dataset_collection.m4v + + +Zip file +-------- + +This method isn't recommended because zip file aren't really well integrated + +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 + | **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). + | 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). + | 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 -For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org). +Raw file format +--------------- -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 to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xcms 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** + | **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 ---------- @@ -475,28 +451,16 @@ Output files ------------ -xset.TICs_raw.pdf - - | "Total Ion Chromatograms" graph in pdf format. - -xset.BPCs_raw.pdf - - | "Base Peak Chromatograms" graph in pdf format with each class samples opposed. - -sampleMetadata.tsv - - | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed). - | This file is necessary in the Anova and PCA step of the workflow. - xset.RData: rdata.xcms.raw format | Rdata file that is necessary in the second step of the workflow "xcms.group". ------- +@HELP_BCP_TIC@ -.. class:: infomark +sampleMetadata.tsv [if using zip] -The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool. + | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed). + | This file is necessary in the Batch correction and statictics steps of the workflow. --------------------------------------------------- @@ -507,49 +471,20 @@ Input files ----------- - | zip_file -> **sacuri.zip** + | Dataset Collection -> build using this dataset_ + +.. _dataset: http://download.workflow4metabolomics.org/datasets/sacurine-neg-subset_mzXML.zip Parameters ---------- - | Method -> **matchedFilter** - | step -> **0.01** - | fwhm -> **4** - | Advanced option -> **show** - | max: -> **50** - | snthresh -> **1** - | steps -> **2** - - -Output files ------------- - - | **1) xset.RData: RData file** - - | **2) Example of a sampleMetadata.tsv :** - - -+---------------------------+------------+---------+ -| sampleMetadata | class | polarity| -+===========================+============+=========+ -|HU_neg_017 | bio |negative | -+---------------------------+------------+---------+ -|HU_neg_028 | bio |negative | -+---------------------------+------------+---------+ -|HU_neg_034 | bio |negative | -+---------------------------+------------+---------+ -|Blanc04 | blank |negative | -+---------------------------+------------+---------+ -|Blanc06 | blank |negative | -+---------------------------+------------+---------+ -|Blanc09 | blank |negative | -+---------------------------+------------+---------+ - - - - | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :** - -.. image:: xcms_tics.png + | **Method**: centWave + | **Max tolerated ppm m/z deviation in consecutive scans in ppm**: 25 + | **Min,Max peak width in seconds**: 10,40 + | **Advanced option**: show + | **Signal/Noise threshold**: 50 + | **Minimum difference in m/z for peaks with overlapping retention times**: 1 + | **Prefilter step for the first phase**: 3,100 --------------------------------------------------- @@ -557,6 +492,10 @@ Changelog/News -------------- +**Version 2.2.0 - 19/10/2017** + +- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC. + **Version 2.1.0 - 22/02/2017** - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group". @@ -593,7 +532,7 @@ - TEST: refactoring to feed the new report tool -**Version 2.0.2 - 18/01/2016 +**Version 2.0.2 - 18/01/2016** - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.