Mercurial > repos > lecorguille > mnsbase_readmsdata
diff msnbase_readmsdata.xml @ 0:3f0a218e2ebc draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
| author | lecorguille |
|---|---|
| date | Tue, 03 Apr 2018 11:45:58 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msnbase_readmsdata.xml Tue Apr 03 11:45:58 2018 -0400 @@ -0,0 +1,243 @@ +<tool id="mnsbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.0"> + <description>Imports mass-spectrometry raw data files</description> + + <macros> + <import>macros.xml</import> + <import>macros_msnbase.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + <command><![CDATA[ + @COMMAND_RSCRIPT@/msnbase_readmsdata.r + + #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"): + singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' + #else + zipfile '$input' + #end if + + @COMMAND_LOG_EXIT@ + ]]></command> + + <inputs> + + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> + + </inputs> + + <outputs> + <data name="xsetRData" format="rdata.msnbase.raw" label="${input.name.rsplit('.',1)[0]}.raw.RData" from_work_dir="readmsdata.RData" /> + <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" > + <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> + </data> + </outputs> + + <tests> + + <test> + <param name="input" value="faahKO_reduce.zip" ftype="zip" /> + <assert_stdout> + <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" /> + <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" /> + <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" /> + <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" /> + <has_text text="faahKO_reduce/KO/ko15.CDF ko15 KO" /> + <has_text text="faahKO_reduce/KO/ko16.CDF ko16 KO" /> + <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" /> + <has_text text="faahKO_reduce/WT/wt16.CDF wt16 WT" /> + </assert_stdout> + <output name="sampleMetadata" value="sampleMetadata.tsv" /> + </test> + <test> + <param name="input" value="ko15.CDF" ftype="netcdf" /> + <assert_stdout> + <has_text text="rowNames: ./ko15.CDF" /> + <has_text text="ko15.CDF" /> + <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" /> + <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" /> + <has_text text="./ko15.CDF ko15 ." /> + </assert_stdout> + </test> + <!-- DISABLE FOR TRAVIS + Useful to generate test-data for the further steps + <test> + <param name="input" value="ko16.CDF" ftype="netcdf" /> + <assert_stdout> + <has_text text="rowNames: ./ko16.CDF" /> + <has_text text="ko16.CDF" /> + <has_text text="./ko16.CDF ko16 ." /> + </assert_stdout> + </test> + <test> + <param name="input" value="wt15.CDF" ftype="netcdf" /> + <assert_stdout> + <has_text text="rowNames: ./wt15.CDF" /> + <has_text text="wt15.CDF" /> + <has_text text="./wt15.CDF wt15 ." /> + </assert_stdout> + </test> + <test> + <param name="input" value="wt16.CDF" ftype="netcdf" /> + <assert_stdout> + <has_text text="rowNames: ./wt16.CDF" /> + <has_text text="wt16.CDF" /> + <has_text text="./wt16.CDF wt16 ." /> + </assert_stdout> + </test> + --> + </tests> + + <help><![CDATA[ + +@HELP_AUTHORS@ + +================== +MSnbase readMSData +================== + +----------- +Description +----------- + +Reads as set of XML-based mass-spectrometry data files and +generates an MSnExp object. This function uses the functionality +provided by the ‘mzR’ package to access data and meta data in +‘mzData’, ‘mzXML’ and ‘mzML’. + +.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html +.. _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 +========================= ================= ======= ========= + + +**Downstream tools** + +=========================== ==================== ==================== +Name Output file Format +=========================== ==================== ==================== +xcms.findChromPeaks xset.RData rdata.msnbase.raw +--------------------------- -------------------- -------------------- +PCA ellipsoid by factors sampleMetadata.tsv Tabular +--------------------------- -------------------- -------------------- +Anova sampleMetadata.tsv Tabular +=========================== ==================== ==================== + + + +**Example of a metabolomic workflow** + +.. image:: mnsbase_readmsdata_workflow.png + +--------------------------------------------------- + + + +----------- +Input files +----------- + +=========================== ================================== +Parameter : num + label Format +=========================== ================================== +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). + +Zip file: 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, otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug). + +.. _7Zip: http://www.7-zip.org/ + +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. + +.. _HOWTO: 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** + + +------------ +Output files +------------ + +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.msnbase.raw format + + | Rdata file that is necessary in the second step of the workflow "xcms.findChromPeaks". + +--------------------------------------------------- + +Changelog/News +-------------- + + +**Version 2.4.0.0 - 29/03/2018** + +- NEW: a new dedicated tool to read the raw data. This function was previously included in xcms.findChromPeaks. This way, you will now be able to display TICs and BPCs before xcms.findChromPeaks. + + ]]></help> + + <expand macro="citation" /> +</tool>