Mercurial > repos > ethevenot > batchcorrection
diff determine_bc.xml @ 0:b74d1d533dea draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
| author | ethevenot |
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| date | Thu, 04 Aug 2016 11:40:35 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/determine_bc.xml Thu Aug 04 11:40:35 2016 -0400 @@ -0,0 +1,283 @@ +<tool id="Determine_BC" name="Determine_batch_correction" version="2.0.0"> + <description>to choose between linear, lowess and loess methods</description> + + <requirements> + <requirement type="package" version="3.3.1">R</requirement> + <requirement type="package">r-batch</requirement> + <requirement type="package">r-ade4</requirement> + <requirement type="package">r-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="hide"> + <param name="span" type="hidden" value="none"/> + </when> + <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** Franck Giacomoni and Marion Landi (for interface and wrapper) and Jean-Francois Martin and Melanie Petera (for R) + +--------------------------------------------------- + +.. 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:: ./static/images/metabolomics/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 + +Soon see the corresponding "Page" + + +</help> + +<citations> + <citation type="bibtex">@Article{Kloet2009, + Title = {Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping}, + Author = {van der Kloet, Frans M. and Bobeldijk, Ivana and Verheij, Elwin R. and Jellema, Renger H.}, + Journal = {Journal of Proteome Research}, + Year = {2009}, + Note = {PMID: 19754161}, + Number = {11}, + Pages = {5132-5141}, + Volume = {8}, + + Doi = {10.1021/pr900499r}, + Url = {http://pubs.acs.org/doi/abs/10.1021/pr900499r} + }</citation> + <citation type="doi">10.1093/bioinformatics/btu813</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>