Mercurial > repos > lecorguille > anova
diff abims_anova.xml @ 9:4f06e1796334 draft
planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
| author | lecorguille |
|---|---|
| date | Thu, 26 Oct 2017 09:30:56 -0400 |
| parents | |
| children | b147b17759a6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_anova.xml Thu Oct 26 09:30:56 2017 -0400 @@ -0,0 +1,269 @@ +<tool id="abims_anova" name="Anova" version="1.1.4"> + + <description>N-way anova. With ou Without interactions</description> + + <requirements> + <requirement type="package" version="1.1_4">r-batch</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command> +Rscript $__tool_directory__/abims_anova.r file '$input' sampleinfo '$sampleinfo' mode '$mode' +condition "c('$condition_1' +#for $i, $s in enumerate( $conditions ) +,'${s.condition}' +#end for +)" +interaction $interaction +method $method +threshold $threshold +selection_method $selection_method +sep '$sep' +dec '$dec' +outputdatapvalue '$dataMatrixPValue' +outputdatafiltered '$dataMatrixFiltered' + </command> + + <inputs> + <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." /> + <param name="sampleinfo" type="data" label="Sample Metadata file" format="tabular" help="Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition" /> + + <param name="mode" type="select" help="Perform the anova tests on column/row" format="text" optional="true"> + <label>Mode</label> + <option value="row">row</option> + <option value="column">column</option> + </param> + + <param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" /> + <repeat name="conditions" title="Conditions for N-ways anova"> + <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" /> + </repeat> + + <param name="interaction" type="boolean" label="Enable interaction response p-values" truevalue="T" falsevalue="F" help="Used if more than 1 conditon. The anova will produse p-value according to the interaction between your condition (ex: condition1:conditions2, condition1:conditions3, condition2:conditions3 and condition1:condition2:conditions3)" /> + + <param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" > + <label>PValue adjusted method</label> + <option value="BH">BH</option> + <option value="holm">holm</option> + <option value="bonferroni">bonferroni</option> + <option value="hochberg">hochberg</option> + <option value="hommel">hommel</option> + <option value="BY">BY</option> + <option value="fdr">fdr</option> + <option value="none">none</option> + </param> + + <param name="threshold" type="float" label="Threshold" value="0.01" help="max adjusted p.value accepted" /> + + <param name="selection_method" type="select" help="Intersection: all condition p-value must be under the threshold. Union: at least condition p-value must be under the threshold. "> + <label>Selection method</label> + <option value="intersection" selected="true">intersection / strong</option> + <option value="union">union / weak</option> + </param> + + <param name="sep" type="select" format="text"> + <label>Separator of columns</label> + <option value="tabulation">tabulation</option> + <option value="semicolon">;</option> + <option value="comma">,</option> + </param> + + <param name="dec" type="text" label="Decimal separator" value="." help="" /> + + </inputs> + + <outputs> + <data name="dataMatrixPValue" format_source="input" label="${input.name}_anova_pvalue.${input.ext}"/> + <data name="dataMatrixFiltered" format_source="input" label="${input.name}_anova_filtered.${input.ext}"/> + </outputs> + + <tests> + <test> + <param name="input" value="dataMatrix.tsv"/> + <param name="sampleinfo" value="sampleMetadata.tsv"/> + <param name="mode" value="row"/> + <param name="condition_1" value="age"/> + <param name="conditions_0|condition" value="gender"/> + <param name="interaction" value="F"/> + <param name="method" value="BH"/> + <param name="threshold" value="0.05"/> + <param name="selection_method" value="union"/> + <param name="sep" value="tabulation"/> + <param name="dev" value="."/> + <output name="dataMatrixPValue" file="dataMatrix.tsv_anova_pvalue.tabular" /> + <output name="dataMatrixFiltered" file="dataMatrix.tsv_anova_filtered.tabular" /> + </test> + </tests> + + <help> + +.. class:: infomark + +**Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr + +--------------------------------------------------- + +===== +Anova +===== + +----------- +Description +----------- + +Analysis of variance (ANOVA) is used to analyze the differences between group means and their associated procedures, +in which the observed variance in a particular variable is partitioned into components attributable to different sources of variation. + + + +----------- +Input files +----------- + ++---------------------------+------------+ +| Parameter : num + label | Format | ++===========================+============+ +| 1 : Data Matrix file | Tabular | ++---------------------------+------------+ +| 2 : Sample Metadata file | Tabular | ++---------------------------+------------+ + + + +------------ +Output files +------------ + + + +***.anova_pvalue.tabular** + + | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue). + +***.anova_filtered.tabular** + + | The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue. + + +------ + +.. class:: infomark + +The outputs ***.anova_filtered.tabular** or ***.anova_pvalue.tabular** are tabular files. You can continue your analysis using it in the following tools: + + | PCA + | Hierarchical Clustering + + + +--------------------------------------------------- + +--------------- +Working example +--------------- + + +Input files +----------- + +**>A part of an example of Data Matrix file input** + + ++--------+------------------+----------------+ +| Name | Bur-eH_FSP_12 | Bur-eH_FSP_24 | ++========+==================+================+ +|M202T601| 91206595.7559783 |106808979.08546 | ++--------+------------------+----------------+ +|M234T851| 27249137.275504 |28824971.3177926| ++--------+------------------+----------------+ + +**>A part of an example of Sample Metadata file input** + + ++---------------------------+------------+------------+------------+ +| Sample name | class | time | batch | ++===========================+============+============+============+ +| Bur-eH_FSP_12 | Bur-eH | 12 | 1 | ++---------------------------+------------+------------+------------+ +| Bur-eH_FSP_24 | Bur-eH | 24 | 1 | ++---------------------------+------------+------------+------------+ +| Bur-NI_FSP_12 | Bur-NI | 12 | 2 | ++---------------------------+------------+------------+------------+ +| Bur-NI_FSP_24 | Bur-NI | 24 | 2 | ++---------------------------+------------+------------+------------+ + +Parameters +---------- + + | Mode -> **row** + | column name of condition -> **class** + | Separator of columns: -> **tabulation** + | Decimal separator -> **.** + | PValue adjusted method -> **BH** + | Threshold -> **0.001** + + + +Output files +------------ + +**Part of an example of xset.anova_filtered.tabular:** + +.. image:: anova_pvalue.png + +**Part of an example of xset.anova_pvalue.tabular:** + +.. image:: anova_filtered.png + + +--------------------------------------------------- + + +--------------------------- +Position in workflow4metabo +--------------------------- + + +**Upstream tools** + ++---------------------------+----------------------------------------+--------+------------------------+ +| Name | Output file | Format | parameter | ++===========================+========================================+========+========================+ +|CAMERA.annotateDiffreport |xset.annotatediffreport.data_matrix.tsv | Tabular| Data table file | ++---------------------------+----------------------------------------+--------+------------------------+ +|xcms.xcmsSet |sample_info.tab | Tabular| sample info table file | ++---------------------------+----------------------------------------+--------+------------------------+ + + +**Downstream tools** + ++---------------------------+---------------------------------------------------------+--------+ +| Name | Output file | Format | ++===========================+=========================================================+========+ +|PCA |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular| ++---------------------------+---------------------------------------------------------+--------+ +|Hierarchical Clustering |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular| ++---------------------------+---------------------------------------------------------+--------+ + + +**General schema of the metabolomic workflow** + +.. image:: anova_workflow.png + + </help> + + <citations> + <citation type="bibtex">@ARTICLE{fisher, + author = {Ronald A. Fisher}, + title = {The Correlation between Relatives on the Supposition of Mendelian Inheritance}, + journal = {Philosophical Transactions of the Royal Society of Edinburgh}, + year = {1918}, + volume = {52}, + pages = {399-433} + }</citation> + </citations> + +</tool>