Mercurial > repos > lecorguille > ipo
diff ipo4xcmsSet.xml @ 9:364756ea5f42 draft
"planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
| author | workflow4metabolomics |
|---|---|
| date | Mon, 16 Dec 2019 10:26:13 +0000 |
| parents | dd0a593dded1 |
| children | 57f180a8eaae |
line wrap: on
line diff
--- a/ipo4xcmsSet.xml Thu Aug 03 05:56:58 2017 -0400 +++ b/ipo4xcmsSet.xml Mon Dec 16 10:26:13 2019 +0000 @@ -1,43 +1,17 @@ -<tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="0.0.3"> +<tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="@TOOL_VERSION@+galaxy0"> - <description>IPO optimization process for xcms.xcmsSet</description> + <description>IPO optimization process for xcms.findChromPeaks</description> <macros> <import>macros.xml</import> - - <macro name="centwave_ppm_fixed"> - <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" /> - </macro> - <macro name="centwave_peakwidth_fixed"> - <param name="min_peakwidth" type="float" value="20" label="Min peak width range in seconds" optional="true" help="[min_peakwidth]" /> - <param name="max_peakwidth" type="float" value="50" label="Max peak width range in seconds" optional="true" help="[max_peakwidth]" /> - </macro> - <macro name="centwave_mzdiff_fixed"> - <param name="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] Can be negative to allow overlap" /> - </macro> - - <macro name="matchedfilter_fwhm_fixed"> - <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" /> - </macro> - <macro name="matchedfilter_mzdiff_fixed"> - <param name="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps " /> - </macro> </macros> <expand macro="requirements"/> - <expand macro="stdio"/> - - <command><![CDATA[ - LANG=C Rscript $__tool_directory__/ipo4xcmsSet.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 detect_errors="exit_code"><![CDATA[ + LANG=C Rscript '$__tool_directory__/ipo4xcmsSet.r' - parametersOutput $parametersOutput - xsetRdataOutput $xsetRData + singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' samplebyclass $samplebyclass @@ -45,10 +19,10 @@ @COMMAND_NSLAVES@ method $methods.method #if $methods.method == "centWave": - ppm "c($methods.section_centwave_optiomizable.conditional_parameter.ppm)" - min_peakwidth "c($methods.section_centwave_optiomizable.conditional_parameter.min_peakwidth)" - max_peakwidth "c($methods.section_centwave_optiomizable.conditional_parameter.max_peakwidth)" - mzdiff "c($methods.section_centwave_optiomizable.conditional_parameter.mzdiff)" + ppm "c($methods.section_centwave_optiomizable.ppm)" + min_peakwidth "c($methods.section_centwave_optiomizable.min_peakwidth)" + max_peakwidth "c($methods.section_centwave_optiomizable.max_peakwidth)" + mzdiff "c($methods.section_centwave_optiomizable.mzdiff)" snthresh $methods.section_centwave_non_optiomizable.snthresh integrate $methods.section_centwave_non_optiomizable.integrate @@ -56,26 +30,24 @@ prefilter "c($methods.section_centwave_non_optiomizable.prefilter)" #elif $methods.method == "matchedFilter": - fwhm "c($methods.section_matchedfilter_optiomizable.conditional_parameter.fwhm)" - mzdiff "c($methods.section_matchedfilter_optiomizable.conditional_parameter.mzdiff)" + fwhm "c($methods.section_matchedfilter_optiomizable.fwhm)" + mzdiff "c($methods.section_matchedfilter_optiomizable.mzdiff)" step $methods.section_matchedfilter_non_optimizable.step steps $methods.section_matchedfilter_non_optimizable.steps max $methods.section_matchedfilter_non_optimizable.max snthresh $methods.section_matchedfilter_non_optimizable.snthresh #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." /> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. See the help section below." /> <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" /> <conditional name="methods"> - <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below"> + <param argument="method" type="select" label="Extraction method for peaks detection (findChromPeaks)" help="See the help section below"> <option value="centWave" >centWave</option> <option value="matchedFilter" selected="true">matchedFilter</option> </param> @@ -83,78 +55,47 @@ <!-- centWave Filter options --> <when value="centWave"> <section name="section_centwave_optiomizable" title="Optimizable parameters" expanded="True"> - <conditional name="conditional_parameter"> - <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values"> - <option value="ppm">Max tolerated ppm m/z deviation in consecutive scans in ppm [ppm]</option> - <option value="peakwidth">Min,Max peak width in seconds [peakwidth]</option> - <option value="mzdiff">Minimum difference in m/z for peaks with overlapping Retention Times [mzdiff]</option> - </param> - <when value="ppm"> - <param name="ppm" type="text" value="17,32" label="Range for Max tolerated ppm m/z deviation in consecutive scans in ppm" optional="false" help="[ppm] (ex: 25 or 17,32)"> - <validator type="regex" message="Should be this format XX,YY">[0-9]+,[0-9]+</validator> - </param> - <expand macro="centwave_peakwidth_fixed" /> - <expand macro="centwave_mzdiff_fixed" /> - </when> - <when value="peakwidth"> - <param name="min_peakwidth" type="text" value="12,18" label="Range for Min peak width range in seconds" optional="true" help="[min_peakwidth] (ex: 12,18)"> - <validator type="regex" message="Should be one combinaison of those format: XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,[0-9]+[\.]?[0-9]*</validator> - </param> - <param name="max_peakwidth" type="text" value="35,65" label="Range for Max peak width range in seconds" optional="true" help="[max_peakwidth] (ex: 35,65)"> - <validator type="regex" message="Should be one combinaison of those format: XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,[0-9]+[\.]?[0-9]*</validator> - </param> - <expand macro="centwave_ppm_fixed" /> - <expand macro="centwave_mzdiff_fixed" /> - </when> - <when value="mzdiff"> - <param name="mzdiff" type="text" value="-0.001,0.010" label="Range for Minimum difference in m/z for peaks with overlapping retention times" help="[mzdiff] Can be negative to allow overlap (ex: -0.001,0.010)"> - <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator> - </param> - <expand macro="centwave_ppm_fixed" /> - <expand macro="centwave_peakwidth_fixed" /> - </when> - </conditional> + <param argument="ppm" type="text" value="17,32" label="Range or a fixed value for Max tolerated ppm m/z deviation in consecutive scans in ppm" optional="false" help="(ex: 25 or 17,32)"> + <expand macro="input_validator_range_integer"/> + </param> + <param argument="min_peakwidth" type="text" value="12,18" label="Range or a fixed value for Min peak width range in seconds" optional="true" help="(ex: 12,18)"> + <expand macro="input_validator_range_float"/> + </param> + <param argument="max_peakwidth" type="text" value="35,65" label="Range or a fixed value for Max peak width range in seconds" optional="true" help="(ex: 35,65)"> + <expand macro="input_validator_range_float"/> + </param> + <param argument="mzdiff" type="text" value="-0.001,0.010" label="Range or a fixed value for Minimum difference in m/z for peaks with overlapping retention times" help="Can be negative to allow overlap (ex: -0.001,0.010)"> + <expand macro="input_validator_range_float_neg"/> + </param> </section> <section name="section_centwave_non_optiomizable" title="Non optimizable parameters" expanded="True"> - <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" /> - <param name="integrate" type="select" label="Peak limits method" help="[integrate]" > + <param argument="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="Signal to noise ratio cutoff" /> + <param argument="integrate" type="select" label="Peak limits method" > <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option> <option value="2">peak limits based on real data (more sensitive to noise)</option> </param> - <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/> - <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/> + <param argument="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/> + <param argument="noise" type="integer" value="0" label="Noise filter" help="optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/> </section> </when> <!-- matched Filter options --> <when value="matchedFilter"> <section name="section_matchedfilter_optiomizable" title="Optimizable parameters" expanded="True"> - <conditional name="conditional_parameter"> - <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values"> - <option value="fwhm">Full width at half maximum of matched filtration gaussian model peak [fwhm]</option> - <option value="mzdiff">Minimum difference in m/z for peaks with overlapping Retention Times [mzdiff]</option> - </param> - <when value="fwhm"> - <param name="fwhm" type="text" value="25,35" label="Range for Full width at half maximum of matched filtration gaussian model peak" optional="true" help="[fwhm] Only used to calculate the actual sigma (ex: 25,35)"> - <validator type="regex" message="Should be this format: XX,YY">[0-9]+,[0-9]+</validator> - </param> - <expand macro="matchedfilter_mzdiff_fixed" /> - </when> - <when value="mzdiff"> - <param name="mzdiff" type="text" value="0.4,0.7" label="Range for Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps (ex: 0.4,0.7)"> - <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator> - </param> - <expand macro="matchedfilter_fwhm_fixed" /> - </when> - </conditional> + <param argument="fwhm" type="text" value="25,35" label="Range or a fixed value for Full width at half maximum of matched filtration gaussian model peak" optional="true" help="Only used to calculate the actual sigma (ex: 25,35)"> + <expand macro="input_validator_range_integer"/> + </param> + <param argument="mzdiff" type="text" value="0.4,0.7" label="Range or a fixed value for Minimum difference in m/z for peaks with overlapping Retention Times" help="By default: 0.8-step*steps (ex: 0.4,0.7)"> + <expand macro="input_validator_range_float_neg"/> + </param> </section> <section name="section_matchedfilter_non_optimizable" title="Non optimizable parameters" expanded="True"> - <param name="step" type="float" value="0.1" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> - <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> - <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" /> - <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" /> + <param argument="step" type="float" value="0.1" label="Step size to use for profile generation" help="The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> + <param argument="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> + <param argument="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" /> + <param argument="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" /> </section> </when> </conditional> @@ -163,9 +104,8 @@ </inputs> <outputs> - <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" /> - <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" /> - <data name="log" format="txt" label="ipo4xcmsSet.log.txt" /> + <data name="xsetRData" format="rdata.xcms.raw" label="ipo4xcmsSet.RData" from_work_dir="ipo4xcmsSet.RData" /> + <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" from_work_dir="IPO_parameters4xcmsSet.tsv" /> </outputs> <tests> @@ -175,13 +115,10 @@ <conditional name="methods"> <param name="method" value="centWave" /> <section name="section_centwave_optiomizable" > - <conditional name="conditional_parameter"> - <param name="select_parameter" value="peakwidth" /> - <param name="min_peakwidth" value="3,9.5" /> - <param name="max_peakwidth" value="10,20" /> - <param name="ppm" value="56" /> - <param name="mzdiff" value="-0.001" /> - </conditional> + <param name="min_peakwidth" value="3,9.5" /> + <param name="max_peakwidth" value="10,20" /> + <param name="ppm" value="56" /> + <param name="mzdiff" value="-0.001" /> </section> </conditional> <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet_peakwidth.tsv" /> @@ -192,51 +129,29 @@ <conditional name="methods"> <param name="method" value="centWave" /> <section name="section_centwave_optiomizable" > - <conditional name="conditional_parameter"> - <param name="select_parameter" value="ppm" /> - <param name="ppm" value="50,60" /> - <param name="min_peakwidth" value="3.325" /> - <param name="max_peakwidth" value="11" /> - <param name="mzdiff" value="-0.001" /> - </conditional> + <param name="ppm" value="50,60" /> + <param name="min_peakwidth" value="3.325" /> + <param name="max_peakwidth" value="11.0" /> + <param name="mzdiff" value="-0.001" /> </section> </conditional> - <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet_ppm.tsv" /> + <output name="parametersOutput"> + <assert_contents> + <!-- 	 is XML escape code for tab --> + <has_line line="ppm	60" /> + <has_line line="min_peakwidth	3.325" /> + <has_line line="max_peakwidth	11" /> + <has_line line="mzdiff	-0.001" /> + <has_line line="prefilter	3" /> + <has_line line="snthresh	10" /> + <has_line line="integrate	1" /> + <has_line line="noise	0" /> + <has_line line="value_of_prefilter	100" /> + <has_line line="mzCenterFun	wMean" /> + <has_line line="fitgauss	FALSE" /> + </assert_contents> + </output> </test> - <!-- Too long for Travis CI --> - <!--<test> - <param name="inputs|input" value="zip_file" /> - <param name="inputs|zip_file" value="sacuri_2files.zip" ftype="zip" /> - <param name="samplebyclass" value="1" /> - <param name="methods|method" value="centWave" /> - <param name="methods|ppm" value="25" /> - <param name="methods|min_peakwidth" value="20,30" /> - <param name="methods|max_peakwidth" value="45,55" /> - <output name="parametersOutput" file="sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv" /> - </test>--> - <!-- Too long for Travis CI --> - <!--<test> - <param name="inputs|input" value="zip_file" /> - <param name="inputs|zip_file" value="sacuri_2files.zip" ftype="zip" /> - <param name="samplebyclass" value="1" /> - <param name="methods|method" value="matchedFilter" /> - <param name="methods|step" value="0.05,0.15" /> - <param name="methods|fwhm" value="25,35" /> - <output name="parametersOutput" file="sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv" /> - </test>--> - <!--Failed: - Error in resultIncreased(history) : - No isotopes have been detected, peak picking not optimizable by IPO!--> - <!--<test> - <param name="inputs|input" value="zip_file" /> - <param name="inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> - <param name="methods|method" value="centWave" /> - <param name="methods|ppm" value="25" /> - <param name="methods|min_peakwidth" value="15,25" /> - <param name="methods|min_peakwidth" value="20,30" /> - <param name="methods|max_peakwidth" value="45,55" /> - <output name="parametersOutput" file="faahKO_IPO_parameters4xcmsSet.tsv" /> - </test>--> </tests> <help><![CDATA[ @@ -260,11 +175,13 @@ **Upstream tools** -========================= ================= ======= ========= -Name output file format parameter -========================= ================= ======= ========= -NA NA zip NA -========================= ================= ======= ========= +========================= ======================== +Name Format +========================= ======================== +Upload File mzxml,mzml,mzdata,netcdf +========================= ======================== + +The easier way to process is to create a Dataset Collection of the type List **Downstream tools** @@ -281,43 +198,6 @@ Input files ----------- -+---------------------------+------------+ -| Parameter : num + label | Format | -+===========================+============+ -| 1 : Choose your inputs | zip | -+---------------------------+------------+ - -**Choose your inputs** - -You have two methods for your inputs: - - | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). - | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories. - -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 - -**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 (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 ---------------------------------------------------- @@ -344,37 +224,30 @@ Parameters ---------- -Extraction method for peaks detection +Extraction method for findChromPeaks ------------------------------------- -**Matched Filter** - - | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. - | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002). +**MatchedFilter** + | The matchedFilter algorithm identifies peaks in the chromatographic time domain as described in [Smith 2006]. The intensity values are binned by cutting The LC/MS data into slices (bins) of a mass unit (‘binSize’ m/z) wide. Within each bin the maximal intensity is selected. The chromatographic peak detection is then performed in each bin by extending it based on the ‘steps’ parameter to generate slices comprising bins ‘current_bin - steps +1’ to ‘current_bin + steps - 1’. Each of these slices is then filtered with matched filtration using a second-derative Gaussian as the model peak shape. After filtration peaks are detected using a signal-to-ratio cut-off. For more details and illustrations see [Smith 2006]. + | See the MatchedFilter_manual_ -**cent Wave** +**CentWave** - | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode. + | The centWave algorithm perform peak density and wavelet based chromatographic peak detection for high resolution LC/MS data in centroid mode [Tautenhahn 2008]. | Due to the fact that peak centroids are used, a binning step is not necessary. | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals. - + | See the CentWave_manual_ ------------- -Output files ------------- - -IPO_parameters4xcmsSet.tsv - - | Optimal parameters for xcmsSet - +.. _MatchedFilter_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-matchedFilter.html#heading-2 +.. _CentWave_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWave.html#heading-2 --------------------------------------------------- Changelog/News -------------- - +@HELP_NEWVERSION_1_10_0_0@ ]]></help>