Mercurial > repos > lecorguille > anova
diff abims_anova.xml @ 10:b147b17759a6 draft
planemo upload for repository https://github.com/workflow4metabolomics/anova commit 28838bb8dafd6d286157db77f181ed8a1b586664
| author | lecorguille |
|---|---|
| date | Wed, 28 Feb 2018 07:44:13 -0500 |
| parents | 4f06e1796334 |
| children | 102049093b7d |
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--- a/abims_anova.xml Thu Oct 26 09:30:56 2017 -0400 +++ b/abims_anova.xml Wed Feb 28 07:44:13 2018 -0500 @@ -1,9 +1,10 @@ -<tool id="abims_anova" name="Anova" version="1.1.4"> - +<tool id="abims_anova" name="Anova" version="1.2.0"> + <description>N-way anova. With ou Without interactions</description> - + <requirements> <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="1.2">r-venn</requirement> </requirements> <stdio> @@ -11,39 +12,40 @@ </stdio> <command> -Rscript $__tool_directory__/abims_anova.r file '$input' sampleinfo '$sampleinfo' mode '$mode' +Rscript $__tool_directory__/abims_anova.r file '$input' sampleinfo '$sampleinfo' varinfo '$varinfo' 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> +interaction $interaction +method $method +threshold $threshold +selection_method $selection_method +sep '$sep' +dec '$dec' +outputdatapvalue '$varMetaPValue' +outputdatasignif '$dataSignif' + </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"> + <param name="varinfo" type="data" label="Variable Metadata file" format="tabular" help="Tabular file with information about your tested variables. Only used to aggregate generated information." /> + + <param name="mode" type="select" help="Perform the anova tests on column/row; for W4M 3-tables format, use 'row'." format="text" optional="true"> <label>Mode</label> - <option value="row">row</option> + <option value="row" selected="True">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> @@ -53,9 +55,9 @@ <option value="hommel">hommel</option> <option value="BY">BY</option> <option value="fdr">fdr</option> - <option value="none">none</option> - </param> - + <option value="none" selected="True">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. "> @@ -70,20 +72,21 @@ <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.${input.ext}"/> + <data name="varMetaPValue" format_source="varinfo" label="${varinfo.name}_anova_pvalue.${varinfo.ext}"/> + <data name="dataSignif" format="pdf" label="${input.name}_anova_signif"/> </outputs> - + <tests> <test> <param name="input" value="dataMatrix.tsv"/> <param name="sampleinfo" value="sampleMetadata.tsv"/> + <param name="varinfo" value="variableMetadata.tsv"/> <param name="mode" value="row"/> <param name="condition_1" value="age"/> <param name="conditions_0|condition" value="gender"/> @@ -93,8 +96,8 @@ <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" /> + <output name="varMetaPValue" file="variableMetadata.tsv_anova_pvalue.tabular" /> + <output name="dataSignif" file="dataMatrix.tsv_anova_signif.pdf" compare="sim_size" delta="600" /> </test> </tests> @@ -102,7 +105,8 @@ .. class:: infomark -**Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr +**Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr +Melanie Petera - PFEM ; INRA ; MetaboHUB --------------------------------------------------- @@ -123,14 +127,15 @@ Input files ----------- -+---------------------------+------------+ -| Parameter : num + label | Format | -+===========================+============+ -| 1 : Data Matrix file | Tabular | -+---------------------------+------------+ -| 2 : Sample Metadata file | Tabular | -+---------------------------+------------+ - ++----------------------------+------------+ +| Parameter : num + label | Format | ++============================+============+ +| 1 : Data Matrix file | Tabular | ++----------------------------+------------+ +| 2 : Sample Metadata file | Tabular | ++----------------------------+------------+ +| 3 : Variable Metadata file | Tabular | ++----------------------------+------------+ ------------ @@ -141,118 +146,28 @@ ***.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 + | Your variable metadata file completed with columns of p-values, result of selection method and means of subgroups. -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 +***.anova_signif.pdf** - - ---------------------------------------------------- - ---------------- -Working example ---------------- + | A pdf file containing a Venn diagram and boxplots of significant variables. -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| -+--------+------------------+----------------+ +.. class:: infomark -**>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 ----------- +The outputs ***.anova_filtered.tabular** is a tabular file. You can continue your analysis using it in the following tools: - | Mode -> **row** - | column name of condition -> **class** - | Separator of columns: -> **tabulation** - | Decimal separator -> **.** - | PValue adjusted method -> **BH** - | Threshold -> **0.001** - - + | Generic_filter + | Hierarchical Clustering -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>