Mercurial > repos > ethevenot > biosigner
diff biosigner_config.xml @ 2:b2414be87d4b draft
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
| author | ethevenot |
|---|---|
| date | Sat, 06 Aug 2016 12:17:12 -0400 |
| parents | 4ff502a46189 |
| children | fa80bd02055f |
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--- a/biosigner_config.xml Sat Jul 30 12:21:07 2016 -0400 +++ b/biosigner_config.xml Sat Aug 06 12:17:12 2016 -0400 @@ -1,89 +1,92 @@ -<tool id="biosigner" name="Biosigner" version="2.2.4"> - <description>Molecular signature discovery from omics data</description> - - <requirements> - <requirement type="package" version="3.2.2">R</requirement> - <requirement type="package">r-batch</requirement> - <requirement type="package">bioconductor-biosigner</requirement> - </requirements> - - <command><![CDATA[ - $__tool_directory__/biosigner_wrapper.R - - dataMatrix_in "$dataMatrix_in" - sampleMetadata_in "$sampleMetadata_in" - variableMetadata_in "$variableMetadata_in" - - respC "$respC" - - #if $advCpt.opcC == "full" - methodC "$advCpt.methodC" - bootI "$advCpt.bootI" - tierC "$advCpt.tierC" - pvalN "$advCpt.pvalN" - seedI "$advCpt.seedI" - #end if - - variableMetadata_out "$variableMetadata_out" - figure_tier "$figure_tier" - figure_boxplot "$figure_boxplot" - information "$information" - ]]></command> - - <inputs> - <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" /> - <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> - <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> - <param name="respC" label="Sample classes" type="text" value = "" help="Column of sampleMetadata containing 2 types of strings (e.g., 'case' and 'control')" /> - - <conditional name="advCpt"> - <param name="opcC" type="select" label="Advanced computational parameters" > - <option value="default" selected="true">Use default</option> - <option value="full">Full parameter list</option> - </param> - <when value="default"/> - <when value="full"> - <param name="methodC" label="Classification method(s)" type="select" help=""> - <option value="all" selected="true">all</option> - <option value="plsda">PLS-DA</option> - <option value="randomforest">Random Forest</option> - <option value="svm">SVM</option> - </param> - <param name="bootI" type="integer" value="50" label="Number of bootstraps" help=""/> - <param name="tierC" label="Selection tier(s)" type="select" help=""> - <option value="S" selected="true">S</option> - <option value="A">S+A</option> - </param> - <param name="pvalN" type="float" value="0.05" label="p-value threshold" help="Must be between 0 and 1"/> - <param name="seedI" type="integer" value="0" label="Seed" help="Select an integer (e.g., 123) if you want to obtain exactly the same signatures when re-running the algorithm; 0 means that no seed is selected"/> - </when> - </conditional> - +<tool id="biosigner" name="Biosigner" version="2.2.6"> + <description>Molecular signature discovery from omics data</description> + + <requirements> + <requirement type="package" version="3.2.2">R</requirement> + <requirement type="package">r-batch</requirement> + <requirement type="package">bioconductor-biosigner</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command><![CDATA[ + Rscript $__tool_directory__/biosigner_wrapper.R + + dataMatrix_in "$dataMatrix_in" + sampleMetadata_in "$sampleMetadata_in" + variableMetadata_in "$variableMetadata_in" + + respC "$respC" + + #if $advCpt.opcC == "full" + methodC "$advCpt.methodC" + bootI "$advCpt.bootI" + tierC "$advCpt.tierC" + pvalN "$advCpt.pvalN" + seedI "$advCpt.seedI" + #end if + + variableMetadata_out "$variableMetadata_out" + figure_tier "$figure_tier" + figure_boxplot "$figure_boxplot" + information "$information" + ]]></command> + + <inputs> + <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" /> + <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> + <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> + <param name="respC" label="Sample classes" type="text" value = "" help="Column of sampleMetadata containing 2 types of strings (e.g., 'case' and 'control')" /> + + <conditional name="advCpt"> + <param name="opcC" type="select" label="Advanced computational parameters" > + <option value="default" selected="true">Use default</option> + <option value="full">Full parameter list</option> + </param> + <when value="default"/> + <when value="full"> + <param name="methodC" label="Classification method(s)" type="select" help=""> + <option value="all" selected="true">all</option> + <option value="plsda">PLS-DA</option> + <option value="randomforest">Random Forest</option> + <option value="svm">SVM</option> + </param> + <param name="bootI" type="integer" value="50" label="Number of bootstraps" help=""/> + <param name="tierC" label="Selection tier(s)" type="select" help=""> + <option value="S" selected="true">S</option> + <option value="A">S+A</option> + </param> + <param name="pvalN" type="float" value="0.05" label="p-value threshold" help="Must be between 0 and 1"/> + <param name="seedI" type="integer" value="0" label="Seed" help="Select an integer (e.g., 123) if you want to obtain exactly the same signatures when re-running the algorithm; 0 means that no seed is selected"/> + </when> + </conditional> </inputs> - + <outputs> <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> - <data name="figure_tier" label="${tool.name}__figure-tier.pdf" format="pdf"/> + <data name="figure_tier" label="${tool.name}__figure-tier.pdf" format="pdf"/> <data name="figure_boxplot" label="${tool.name}__figure-boxplot.pdf" format="pdf"/> - <data name="information" label="${tool.name}__information.txt" format="txt"/> + <data name="information" label="${tool.name}__information.txt" format="txt"/> </outputs> <tests> - <test> - <param name="dataMatrix_in" value="dataMatrix.tsv"/> - <param name="sampleMetadata_in" value="sampleMetadata.tsv"/> - <param name="variableMetadata_in" value="variableMetadata.tsv"/> - <param name="respC" value="gender"/> - <param name="opcC" value="full"/> - <param name="methodC" value="all"/> - <param name="bootI" value="5"/> - <param name="tierC" value="S"/> - <param name="pvalN" value="0.05"/> - <param name="seedI" value="123"/> - <output name="variableMetadata_out" file="variableMetadata.out"/> - </test> + <test> + <param name="dataMatrix_in" value="dataMatrix.tsv"/> + <param name="sampleMetadata_in" value="sampleMetadata.tsv"/> + <param name="variableMetadata_in" value="variableMetadata.tsv"/> + <param name="respC" value="gender"/> + <param name="opcC" value="full"/> + <param name="methodC" value="all"/> + <param name="bootI" value="5"/> + <param name="tierC" value="S"/> + <param name="pvalN" value="0.05"/> + <param name="seedI" value="123"/> + <output name="variableMetadata_out" file="variableMetadata.out"/> + </test> </tests> - + <help> .. class:: infomark @@ -96,7 +99,7 @@ **Please cite** -Philippe Rinaudo, Christophe Junot and Etienne A. Thevenot. *biosigner*: A new method for the discovery of restricted and stable molecular signatures from omics data. *submitted*. +Rinaudo P., Boudah S., Junot C. and Thevenot E.A. (2016). *biosigner*: a new method for the discovery of significant molecular signatures from omics data. *Frontiers in Molecular Biosciences*, **3** (http://dx.doi.org/10.3389/fmolb.2016.00026). --------------------------------------------------- @@ -104,7 +107,7 @@ **R package** -The *biosigner* package has been submitted to the bioconductor repository (http://bioconductor.org/packages/biosigner). +The *biosigner* package is available from the bioconductor repository (http://bioconductor.org/packages/biosigner). --------------------------------------------------- @@ -243,7 +246,7 @@ Working example --------------- -See the **W4M00003_diaplasma** in the **Shared Data/Published Histories** menu +See the **W4M00001a_sacurine-subset-statistics** and **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published) @@ -259,18 +262,47 @@ NEWS ---- +CHANGES IN VERSION 2.2.6 +======================== + +INTERNAL MODIFICATIONS + +Minor internal modifications + +CHANGES IN VERSION 2.2.4 +======================== + +INTERNAL MODIFICATIONS + +Creating additional files for planemo and travis running and installation validation + CHANGES IN VERSION 2.2.2 ======================== +INTERNAL MODIFICATIONS + Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3) CHANGES IN VERSION 2.2.1 ======================== +NEW FEATURE + Creation of the tool - </help> +</help> - <citations/> +<citations> + <citation type="bibtex">@Article{Rinaudo2016, + Title = {biosigner: a new method for the discovery of significant molecular signatures from omics data}, + Author = {Rinaudo, Philippe and Boudah, Samia and Junot, Christophe and Thevenot, Etienne A}, + Journal = {Frontiers in Molecular Biosciences}, + Year = {2016}, + Pages = {--}, + Volume = {3}, + Doi = {10.3389/fmolb.2016.00026} + }</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> +</citations> </tool>