Mercurial > repos > melpetera > batchcorrection
diff batchcorrection-57edfd3943ab/determine_bc.xml @ 4:23314e1192d4 draft default tip
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| author | melpetera |
|---|---|
| date | Thu, 14 Jan 2021 09:56:58 +0000 |
| parents | 73892ef177e3 |
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--- a/batchcorrection-57edfd3943ab/determine_bc.xml Tue May 02 09:47:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,284 +0,0 @@ -<tool id="Determine_BC" name="Determine_batch_correction" version="2.1.2"> - <description>to choose between linear, lowess and loess methods</description> - - <requirements> - <requirement type="package">r-batch</requirement> - <requirement type="package">r-ade4</requirement> - <requirement type="package">bioconductor-pcamethods</requirement> - </requirements> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - - <command><![CDATA[ - Rscript $__tool_directory__/batch_correction_wrapper.R - analyse "determine_bc" - sampleMetadata "$sampleMetadata" - dataMatrix "$dataMatrix" - ref_factor "$ref_factor" - #if str($advance.option ) == 'show': - span $advance.span - #else: - span "none" - #end if - out_graph_pdf "$out_graph_pdf" - out_preNormSummary "$out_preNormSummary" - ]]></command> - - <inputs> - <param name="dataMatrix" type="data" label="Data Matrix file " help="" format="tabular" /> - <param name="sampleMetadata" type="data" label="Sample metadata file " help="must contain at least the three following columns: 'batch' + 'injectionOrder' + 'sampleType'" format="tabular" /> - <param name="ref_factor" type="text" label="Factor of interest " help="column name of the factor of interest (often a biological factor); if none, leave 'batch'" value="batch" /> - <conditional name="advance"> - <param name="option" type="select" label="Advanced options" help="should only be put at 'show' if you have good understanding of the span parameter and are willing to adjust it"> - <option value="show">show</option> - <option value="hide" selected="true">hide</option> - </param> - <when value="show"> - <param name="span" type="float" value="0.85" label="span" help="applied to lowess and loess regression"/> - </when> - </conditional> - </inputs> - - <outputs> - <data name="out_graph_pdf" label="Determine_BC_graph" format="pdf" ></data> - <data name="out_preNormSummary" label="Determine_BC_preNormSummary" format="tabular" ></data> - </outputs> - - <tests> - <test> - <param name="dataMatrix" value="input-determinebc-dataMatrix.tsv"/> - <param name="sampleMetadata" value="input-determinebc-sampleMetadata.tsv"/> - <param name="ref_factor" value="batch"/> - <param name="option" value="hide"/> - <param name="span" value="none"/> - <output name="out_preNormSummary" file="output-determinebc-preNormSummary.txt"/> - </test> - </tests> - - <help> - -.. class:: infomark - -**Authors** - | Jean-Francois Martin - PF MetaToul-AXIOM ; INRA ; MetaboHUB (for original version of this tool and overall development of the R script) - -.. class:: infomark - -**Contributors** - | Melanie Petera - PFEM ; INRA ; MetaboHUB (for R wrapper and R script improvement) - -.. class:: infomark - -**Wrapping** - | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for xml interface and R wrapper) - | Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface and R wrapper) - ---------------------------------------------------- - -.. class:: infomark - -**Please cite** If you use this tool, please cite: - | `F.M. van der Kloet, I. Bobeldijk, E.R. Verheij, R.H. Jellema. (2009). "Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping." Journal of Proteome Research p5132-5141 <http://www.ncbi.nlm.nih.gov/pubmed/19754161>`_ - ---------------------------------------------------- - -========================== -Determine_batch_correction -========================== - ------------ -Description ------------ - -| Allows to choose between linear or non-linear (lowess or loess) functions for batch correction -| using quality control pooled samples (QC-pools) with correction algorithm as mentioned by Van Der Kloet (J Prot Res 2009). -| -| Warning : this module does *not* deliver which choice should be made in model type; -| it only provides tools to help users to determine which choice may be appropriate, based on their own expertise. -| -| This tool is meant to be used prior to the Batch_correction tool to help make a choice in parameters, -| but it is not a requirement and thus can be avoided. - - ------------------ -Workflow position ------------------ - -.. image:: determine_batch_correction.png - :width: 800 - - ------------ -Input files ------------ - -+--------------------------+-----------+ -| Parameter : num + label | Format | -+==========================+===========+ -| 1 : Data Matrix file | tabular | -+--------------------------+-----------+ -| 2 : Sample metadata file | tabular | -+--------------------------+-----------+ - - -Data Matrix file must contain the intensity values of the variables. - | First line must contain all the samples' names - | First column must contain all the variables' ID - | - -Sample metadata file must contain at least the three following columns: - | "batch" to identify the batches of analyses - | "injectionOrder" (integers) defining the injection order of all samples (QC-pools as well as analysed samples) - | "sampleType" indicating if a sample ("sample") or a QC-pool ("pool"); each batch needs - | at least 3 QC-pools for intra-batch linear adjustment and 8 for lo(w)ess adjustment - - -.. class:: warningmark - -NO MISSING DATA are allowed - - ----------- -Parameters ----------- - -Factor of interest - | name of the factor (column header) that will be used as a categorical variable for plots. - | (often a biological factor ; if none, leave “batch”). - | This factor does not affect correction calculation. - | - -Advanced options - | should only be put at "show" if you have good understanding of the span parameter and are willing to adjust it. - | - -Span - | - when advanced option is at "hide" (default) - | default is 1 for loess regression and is two times the ratio between number of pools and number of samples for lowess regression. - | - when advanced option is at "show" : - | filled value is used for lowess and loess regression. - - ------------- -Output files ------------- - -Determine_BC_preNormSummary.tabular - | tabular output - | Meaning of results of diagnosis analysis - | 0 : no preliminary-condition problem - | 1 : standard deviation of QC-pools or samples = 0 - | 2 : insufficient number of QC-pools within a batch (n=3 for linear, n=8 for lowess or loess) - | 3 : significant difference between QC-pools and samples means - | 4 : denominator =0 when on 1 pool per batch non-0 - | 5 : (linear regression only) the slopes ratio “QC-pools/samples” is lower than -0.2 - | - -Determine_BC_graph.pdf - | graphical output - | One page per ion. Plots regression curves for all methods allowed and plot.design results regarding the factor of interest. - - ---------------------------------------------------- - ---------------- -Working example ---------------- - - -.. class:: warningmark - -Refer to the corresponding "W4M HowTo" page: - | `MS data processing - Filters and normalisation <http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4e-2016-data_processing.pdf>`_ - | - | - - -</help> - - <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel --> - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="doi">10.1021/pr900499r</citation> - </citations> - -<!-- -Input files -=========== - -| **These two input files can be used in the purview "URL/Text:" of the tool "Get Data/Upload File",** -| **by checking the box "Convert spaces to tabs: YES"** - -Metadata_samples.txt - Model input Sample metadata file:: - - samples idLIMS serie factor01 factor02 batch injectionOrder sampleType - POOL1 POOL1 pool p pool 01_08_2011 1 p - X12588 12588 3 validation 2 01_08_2011 2 s - X17736 17736 3 Q1 1 01_08_2011 3 s - X15432 15432 3 validation 1 01_08_2011 4 s - X17159 17159 3 Q4 1 01_08_2011 5 s - X14325 14325 3 validation 2 01_08_2011 6 s - X17419 17419 3 Q4 1 01_08_2011 7 s - X16437 16437 3 Q4 1 01_08_2011 8 s - X16172 16172 3 Q4 2 01_08_2011 9 s - X16392 16392 3 Q4 2 01_08_2011 10 s - X13875 13875 3 validation 2 01_08_2011 11 s - POOL2 POOL2 pool p pool 01_08_2011 12 p - X13117 13117 3 Q4 2 01_08_2011 13 s - X13341 13341 3 Q1 2 01_08_2011 14 s - X16888 16888 3 Q4 1 01_08_2011 15 s - X17489 17489 3 Q4 2 01_08_2011 16 s - X12718 12718 3 Q1 2 01_08_2011 17 s - X16235 16235 3 Q4 2 01_08_2011 18 s - X16878 16878 3 Q1 1 01_08_2011 19 s - X12701 12701 3 validation 1 01_08_2011 20 s - X16220 16220 3 Q4 2 01_08_2011 21 s - X15635 15635 3 Q4 1 01_08_2011 22 s - - -Intensity_matrix.txt - Model input Matrix Ions file BEFORE IMPLEMENTATION:: - - samples POOL1 X12588 X17736 X15432 X17159 X14325 X17419 X16437 X16172 X16392 X13875 POOL2 X13117 X13341 X16888 X17489 X12718 X16235 X16878 X12701 X16220 X15635 - ion01 188.4140625 219.729126 122.5697632 123.5487671 805.8852539 183.4683838 37.33084106 151.8625488 97.12005615 91.24694824 69.87762451 195.4349365 112.4111938 136.7092285 159.9987793 172.1585693 0 117.5420532 133.6679688 80.05419922 160.0006104 760.0488281 - ion02 82.02575684 87.11358643 79.82391357 80.33862305 83.08575439 94.27703857 76.02288818 77.04394531 76.97564697 84.17669678 81.04943848 86.44024658 84.11865234 83.71282959 77.75219727 79.15936279 75.98492432 78.2835083 78.98760986 73.98388672 72.20550537 82.16448975 - ion03 25.31900024 24.2960968 23.29342651 31.54063416 30.3830719 22.42404175 35.44485474 26.38783264 17.1401825 21.27339172 20.25959778 26.33859253 18.17146301 26.32852173 24.30648804 28.34313965 29.37016296 18.23519897 24.48402405 25.38140869 24.35777283 21.31071472 - ion04 65.87536621 62.68716431 46.60232544 62.77856445 29.53218079 47.59136963 90.13983154 28.35336304 58.74325562 31.39331055 23.32928467 30.39666748 41.43960571 21.27049255 88.1161499 29.36820984 24.30200195 25.00007629 45.60662842 103.293457 37.46994019 87.09295654 - ion05 0 103.728544 279.5808214 884.2333448 824.5072072 434.6439081 764.82768 799.0972595 398.4002569 382.5370891 74.55342827 0 636.6596277 514.3863309 741.690017 412.3166491 660.8996555 57.36593795 102.2085264 455.6403091 548.6145486 515.8412195 - ion06 2711.785156 3465.292969 2469.75 3435.259766 2482.3125 2593.654297 1407.915039 1291.253906 2241.734375 1444.189453 3363.683594 2578.642578 2633.181641 3397.763672 3706.855469 3647.212891 3548.410156 3714.640625 1889.213867 2262.707031 2107.417969 2763.21875 - ion07 164.9023438 192.40625 140.7609863 192.4053955 139.7540283 140.748291 84.60144043 86.1819458 150.762207 89.90411377 207.5949707 164.0512695 149.8706055 186.336792 214.6140137 202.5360107 214.6877441 195.4482422 117.4679565 127.2941895 142.78479 163.0666504 - - -Parameters -========== - -Factor analysis -> **batch** - - -Output files -============ - -out_preNormSummary.tabular: - -====== ============== ============== -labion batch.1.linear batch.1.lowess -====== ============== ============== -ion01 2 2 -ion02 2 2 -ion03 2 2 -ion04 2 2 -ion05 1 1 -... ... ... -====== ============== ============== - - -out_graph_pdf.pdf - -.. image:: ./static/images/metabolomics/pdf_plotsituation.png - :width: 800 ---> - -</tool>