Mercurial > repos > ethevenot > univariate
diff univariate_config.xml @ 2:09799fc16bc6 draft
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
| author | ethevenot |
|---|---|
| date | Sat, 06 Aug 2016 12:42:42 -0400 |
| parents | fdefbc780d2e |
| children | 140290de7986 |
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--- a/univariate_config.xml Sat Jul 30 12:38:02 2016 -0400 +++ b/univariate_config.xml Sat Aug 06 12:42:42 2016 -0400 @@ -1,71 +1,75 @@ -<tool id="Univariate" name="Univariate" version="2.1.2"> +<tool id="Univariate" name="Univariate" version="2.1.4"> <description>Univariate statistics</description> + + <requirements> + <requirement type="package" version="3.2.2">R</requirement> + <requirement type="package">r-batch</requirement> + <requirement type="package">r-PMCMR</requirement> + </requirements> - <requirements> - <requirement type="package" version="3.2.2">R</requirement> - <requirement type="package">r-batch</requirement> - <requirement type="package">r-pmcmr</requirement> - </requirements> - + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <command><![CDATA[ - $__tool_directory__/univariate_wrapper.R - dataMatrix_in "$dataMatrix_in" - sampleMetadata_in "$sampleMetadata_in" - variableMetadata_in "$variableMetadata_in" + Rscript $__tool_directory__/univariate_wrapper.R - facC "$facC" - tesC "$tesC" - adjC "$adjC" - thrN "$thrN" - - variableMetadata_out "$variableMetadata_out" - information "$information" + dataMatrix_in "$dataMatrix_in" + sampleMetadata_in "$sampleMetadata_in" + variableMetadata_in "$variableMetadata_in" + + facC "$facC" + tesC "$tesC" + adjC "$adjC" + thrN "$thrN" + + variableMetadata_out "$variableMetadata_out" + information "$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="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="facC" label="Factor of interest" type="text" help="Name of the column of the sample metadata table corresponding to the qualitative or quantitative variable"/> <param name="tesC" label="Test" type="select" help=""> - <option value="ttest">ttest (qualitative, 2 levels)</option> - <option value="wilcoxon">Wilcoxon test (qualitative, 2 levels)</option> - <option value="anova">Analysis of variance (qualitative, more than 2 levels)</option> - <option value="kruskal">Kruskal-Wallis rank test (qualitative, more than 2 levels)</option> - <option value="pearson">Pearson correlation test (quantitative)</option> - <option value="spearman">Spearman correlation rank test (quantitative)</option> + <option value="ttest">ttest (qualitative, 2 levels)</option> + <option value="wilcoxon">Wilcoxon test (qualitative, 2 levels)</option> + <option value="anova">Analysis of variance (qualitative, more than 2 levels)</option> + <option value="kruskal">Kruskal-Wallis rank test (qualitative, more than 2 levels)</option> + <option value="pearson">Pearson correlation test (quantitative)</option> + <option value="spearman">Spearman correlation rank test (quantitative)</option> </param> <param name="adjC" label="Method for multiple testing correction" type="select" help=""> - <option value="fdr">fdr</option> - <option value="BH">BH</option> - <option value="bonferroni">bonferroni</option> - <option value="BY">BY</option> - <option value="hochberg">hochberg</option> - <option value="holm">holm</option> - <option value="hommel">hommel</option> - <option value="none">none</option> + <option value="fdr">fdr</option> + <option value="BH">BH</option> + <option value="bonferroni">bonferroni</option> + <option value="BY">BY</option> + <option value="hochberg">hochberg</option> + <option value="holm">holm</option> + <option value="hommel">hommel</option> + <option value="none">none</option> </param> <param name="thrN" type="float" value="0.05" label="(Corrected) p-value significance threshold" help="Must be between 0 and 1"/> - </inputs> - + </inputs> + <outputs> <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> - <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="facC" value="ageGroup"/> - <param name="tesC" value="kruskal"/> - <param name="adjC" value="fdr"/> - <param name="thrN" value="0.05"/> - <output name="variableMetadata_out" file="variableMetadata-output.tsv"/> - </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="facC" value="ageGroup"/> + <param name="tesC" value="kruskal"/> + <param name="adjC" value="fdr"/> + <param name="thrN" value="0.05"/> + <output name="variableMetadata_out" file="output-variableMetadata.tsv"/> + </test> </tests> - + <help> .. class:: infomark @@ -200,6 +204,78 @@ Working example --------------- +.. class:: infomark + +See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-subset-complete**, **W4M00002_mtbls2**, **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published) + +--------------------------------------------------- + +---- +NEWS +---- + +CHANGES IN VERSION 2.1.4 +======================== + +NEW FEATURE + +Level names are now separated by '.' instead of '-' previously in the column names of the output variableMetadata table (e.g., 'jour_ttest_J3.J10_fdr' instead of 'jour_ttest_J3-J10_fdr' previously) + +INTERNAL MODIFICATIONS + +Minor internal changes for toolshed export + +CHANGES IN VERSION 2.1.2 +======================== + +INTERNAL MODIFICATIONS + +Minor internal changes for toolshed export + +CHANGES IN VERSION 2.1.1 +======================== + +INTERNAL MODIFICATIONS + +Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples) + +CHANGES IN VERSION 2.0.1 +======================== + +NEW FEATURE + +(corrected) p-value threshold can be set to any value between 0 and 1 + + +</help> + +<citations> + <citation type="bibtex">@Manual{, + title = {R: A Language and Environment for Statistical Computing}, + author = {{R Core Team}}, + organization = {R Foundation for Statistical Computing}, + address = {Vienna, Austria}, + year = {2016}, + url = {https://www.R-project.org/}, + }</citation> + <citation type="bibtex">@Article{Thevenot2015, + Title = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses}, + Author = {Thevenot, Etienne A. and Roux, Aurelie and Xu, Ying and Ezan, Eric and Junot, Christophe}, + Journal = {Journal of Proteome Research}, + Year = {2015}, + Note = {PMID: 26088811}, + Number = {8}, + Pages = {3322-3335}, + Volume = {14}, + + Doi = {10.1021/acs.jproteome.5b00354}, + Url = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354} + }</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + + + Input files =========== @@ -291,28 +367,5 @@ --------------------------------------------------- ----- -NEWS ----- - -CHANGES IN VERSION 2.1.2 -======================== - -Minor internal changes for toolshed export - -CHANGES IN VERSION 2.1.1 -======================== - -Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples) - -CHANGES IN VERSION 2.0.1 -======================== - -(corrected) p-value threshold can be set to any value between 0 and 1 - - - </help> - - <citations/> </tool>