Mercurial > repos > iuc > rgcca
diff rgcca.xml @ 1:4e73ea176c34 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
| author | iuc |
|---|---|
| date | Sun, 18 Jul 2021 18:03:12 +0000 |
| parents | 067d45e6caa9 |
| children |
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--- a/rgcca.xml Tue Jan 12 10:12:04 2021 +0000 +++ b/rgcca.xml Sun Jul 18 18:03:12 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="rgcca" name="RGCCA" version="@TOOL_VERSION@+galaxy0"> +<tool id="rgcca" name="RGCCA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals.</description> @@ -18,39 +18,64 @@ <requirements> <requirement type="package" version="@TOOL_VERSION@">rgccacmd</requirement> + <requirement type="package" version="4.1">r-base</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #set data_paths = ",".join([str(_.file_name) for _ in $blocks]) #set data_names = ",".join([str(_.element_identifier).replace(',', '_') for _ in $blocks]) + #set out_files = str($output_selector).split(",") Rscript '$__tool_directory__/launcher.R' --datasets '${data_paths}' --names '${data_names}' - --o1 '$individual_plot' --o2 '$corcircle' --o3 '$top_variables' --o4 '$ave' --o5 '$design' --o6 '$individual_table' --o7 '$variable_table' --o8 '$rdata' + #if 'individuals' in $out_files + --o1 '$individual_plot' + #end if + #if 'corcircle' in $out_files + --o2 '$corcircle' + #end if + #if 'top_variables' in $out_files + --o3 '$top_variables' + #end if + #if 'ave' in $out_files + --o4 '$ave' + #end if + #if 'design' in $out_files + --o5 '$design' + #end if + #if 'individual_table' in $out_files + --o6 '$individual_table' + #end if + #if 'variable_table' in $out_files + --o7 '$variable_table' + #end if + #if 'rdata' in $out_files + --o8 '$rdata' + #end if $parse.header --separator $parse.separator $analyse.superblock $analyse.scale #if $analyse.tau.bool == 'false' - --penalty $analyse.tau.value + --penalty $analyse.tau.value #else - --penalty $analyse.tau.bool + --penalty $analyse.tau.bool #end if --ncomp $analyse.ncomp --scheme $analyse.scheme #if $analyse.method.family == '1' - --type pca + --type pca #else - --type $analyse.method.type + --type $analyse.method.type #end if #if $analyse.connection - --connection $analyse.connection + --connection $analyse.connection #end if #if $analyse.supervised.learning_mode == 'supervised' - --response $analyse.supervised.block_response + --response $analyse.supervised.block_response #end if #if $graphic.response - --group $graphic.response + --group $graphic.response #end if --compx $graphic.compx --compy $graphic.compy @@ -181,7 +206,7 @@ <option value="individuals" selected="true">Individual plot</option> <option value="corcircle" selected = "true">Corcircle plot</option> <option value="top_variables">Top variables plot</option> - <option value="ave">Averages plot</option> + <option value="ave">Explained variance plot</option> <option value="design">Design plot</option> <option value="individual_table" selected="true">Individual table</option> <option value="variable_table" selected="true">Variable table</option> @@ -225,7 +250,7 @@ <assert_contents> <has_n_columns n="4"/> <has_line_matching - expression='"agriculture.axis1"\s"agriculture.axis2"\s"superblock.axis1"\s"superblock.axis2"'/> + expression='"agriculture.component1"\s"agriculture.component2"\s"superblock.component1"\s"superblock.component2"'/> <has_line_matching expression='^.+(\s\-?\d+.\d+){4}$'/> </assert_contents> @@ -281,7 +306,7 @@ </test> <test expect_num_outputs="8" expect_exit_code="0"> - <expand macro="output_tests" path="2blocks" compx="3" compy="1"/> + <expand macro="output_tests" path="2blocks"/> <param name="blocks" value="agriculture.tsv,politic.tsv"/> <section name="analyse"> <param name="scale" value="false"/> @@ -324,11 +349,12 @@ **Contact:** -arthur.tenenhaus@centralesupelec.fr +etienne.camenen@gmail.com **R package:** -The RGCCA package is available from the CRAN repository (https://cran.r-project.org/web/packages/RGCCA). + | The RGCCA package is available from the CRAN repository (v2.1.2; https://cran.r-project.org/web/packages/RGCCA). + | This tool is based on a version available on github (v3.0; https://github.com/rgcca-factory/RGCCA). --------------------------------------------------- @@ -340,14 +366,14 @@ **Working example** - | From Russett data (RGCCA package): https://github.com/rgcca-factory/RGCCA/tree/master/inst/extdata - | Use *agriculture.tsv* as a block. Add *industry.tsv* and *politic.tsv* as new blocks. *connection.tsv* could be used as a design matrix and *political_system.tsv* as a response variable respectively in analysis and graphic settings. + | From Russett data (RGCCA package): https://github.com/BrainAndSpineInstitute/rgcca_ui/tree/master/inst/extdata + | Use *agriculture.tsv* as a block. Add *industry.tsv* and *politic.tsv* for multiblock analysis. *connection.tsv* could be used as a design matrix and *political_system.tsv* as a response variable respectively in analysis and graphic settings. **Documentation** - RGCCA: https://cran.r-project.org/web/packages/RGCCA/vignettes/vignette_RGCCA.pdf -- accepted input / output formats: https://github.com/rgcca-factory/RGCCA#input-files -<!-- - tutorial: https://github.com/BrainAndSpineInstitute/rgcca_galaxy/blob/release/0.2/README.md--> +- accepted input / https://github.com/BrainAndSpineInstitute/rgcca_ui#input-files +- tutorial: https://github.com/BrainAndSpineInstitute/rgcca_galaxy#readme </help>