rgcca: rgcca.xml annotate

annotate rgcca.xml @ 0:067d45e6caa9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"

author	iuc
date	Tue, 12 Jan 2021 10:12:04 +0000
parents
children	4e73ea176c34

rev	line source
0 067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	1 <tool id="rgcca" name="RGCCA" version="@TOOL_VERSION@+galaxy0">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	2
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	3 <description>performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals.</description>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	4
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	5 <macros>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	6 <import>macro.xml</import>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	7 </macros>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	8
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	9 <edam_topics>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	10 <edam_topic>topic_2269</edam_topic>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	11 </edam_topics>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	12
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	13 <edam_operations>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	14 <edam_operation>operation_2945</edam_operation>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	15 <edam_operation>operation_3465</edam_operation>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	16 <edam_operation>operation_0337</edam_operation>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	17 </edam_operations>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	18
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	19 <requirements>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	20 <requirement type="package" version="@TOOL_VERSION@">rgccacmd</requirement>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	21 </requirements>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	22
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	23 <command detect_errors="exit_code"><![CDATA[
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	24 #set data_paths = ",".join([str(_.file_name) for _ in $blocks])
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	25 #set data_names = ",".join([str(_.element_identifier).replace(',', '_') for _ in $blocks])
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	26 Rscript '$__tool_directory__/launcher.R'
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	27 --datasets '${data_paths}'
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	28 --names '${data_names}'
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	29 --o1 '$individual_plot' --o2 '$corcircle' --o3 '$top_variables' --o4 '$ave' --o5 '$design' --o6 '$individual_table' --o7 '$variable_table' --o8 '$rdata'
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	30 $parse.header
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	31 --separator $parse.separator
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	32 $analyse.superblock
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	33 $analyse.scale
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	34 #if $analyse.tau.bool == 'false'
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	35 --penalty $analyse.tau.value
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	36 #else
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	37 --penalty $analyse.tau.bool
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	38 #end if
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	39 --ncomp $analyse.ncomp
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	40 --scheme $analyse.scheme
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	41 #if $analyse.method.family == '1'
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	42 --type pca
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	43 #else
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	44 --type $analyse.method.type
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	45 #end if
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	46 #if $analyse.connection
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	47 --connection $analyse.connection
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	48 #end if
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	49 #if $analyse.supervised.learning_mode == 'supervised'
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	50 --response $analyse.supervised.block_response
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	51 #end if
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	52 #if $graphic.response
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	53 --group $graphic.response
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	54 #end if
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	55 --compx $graphic.compx
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	56 --compy $graphic.compy
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	57 --nmark $graphic.nmark
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	58 $graphic.text
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	59 --block $graphic.blockx
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	60 --block_y $graphic.blocky
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	61 ]]></command>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	62
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	63 <inputs>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	64 <param name="blocks" type="data" format="tsv,tabular,txt,csv" multiple="true" optional="false" label = "Load blocks"
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	65 help="TSV file containing a matrix with: (i) quantitative values only (decimal should be separated by '.'), (ii) the samples in lines (should be labelled in the 1rst column) and (iii) variables in columns (should have a header)."/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	66
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	67 <section name="parse" title="Advanced parsing" help="By default, on tabulated files with a header.">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	68 <param name="header" type="boolean" truevalue="" falsevalue="-H" checked="true" label="Consider the first row as header of columns" help="Used for both blocks and color files."/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	69 <param name="separator" type="select" display="radio" label="Column separator" help="Character used to separate the column (for all blocks, connection and color files).">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	70 <option value="1" selected="true">Tabulation</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	71 <option value="2">Semicolon</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	72 </param>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	73 </section>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	74
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	75 <section name="analyse" title="Advanced analysis"
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	76 help="By default, the analysis: is a Regularised Generalised Canonical Correlation Analysis, scales the blocks, uses a superblock with a factorial scheme function, a tau equals to one and two components for each block.">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	77
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	78 <param name="ncomp" type="integer" label="Number of component" value="2" min="2" max="5"
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	79 help="The number of component to use in the analysis for each block (should not be greater than the minimum number of variable among the blocks)."/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	80
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	81 <param name="scale" type="boolean" truevalue="" falsevalue="--scale" checked="true" label="Scale the blocks"
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	82 help="A data centering step is always performed. If activated, each block is normalised and divided by the square root of its number of variables."/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	83
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	84 <conditional name="method">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	85
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	86 <param name="family" type="select" label="Analysis method">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	87 <option value="1">One block</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	88 <option value="2">Two blocks</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	89 <option value="m" selected="true">Multiple blocks</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	90 <option value="ms">Multiple blocks with superblock</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	91 </param>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	92
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	93 <when value="2">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	94 <param name="type" type="select" label=" ">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	95 <option value="pls">Partial Least Squares Regression</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	96 <option value="cca">Canonical Correlation Analysis</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	97 <option value="ifa">Interbattery Factor Analysis</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	98 <option value="ra">Redundancy analysis</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	99 </param>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	100 </when>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	101
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	102 <when value="m">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	103 <param name="type" type="select" label=" ">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	104 <option value="rgcca">Regularized Generalized CCA</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	105 <option value="sgcca">Sparse Generalized CCA</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	106 <option value="sumcor">SUM of CORrelations method</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	107 <option value="ssqcor">Sum of SQuared CORrelations method</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	108 <option value="sabscor">Sum of ABSolute value CORrelations method</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	109 <option value="sumcov">SUM of COVariances method</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	110 <option value="ssqcov">Sum of SQuared COVariances method</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	111 <option value="sabscov">Sum of ABSolute value COVariances method</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	112 <option value="maxbet">MAXBET</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	113 <option value="maxbet-b">MAXBET-B</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	114 </param>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	115 </when>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	116
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	117 <when value="ms">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	118 <param name="type" type="select" label=" ">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	119 <option value="gcca">Generalized CCA</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	120 <option value="hpca">Hierarchical PCA</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	121 <option value="mfa">Multiple Factor Analysis</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	122 </param>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	123 </when>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	124
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	125 <when value="1"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	126
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	127 </conditional>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	128
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	129 <param name="connection" optional="true" type="data" format="tsv,tabular,txt,csv" label="Load the design matrix (if superblock or supervised disabled)"
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	130 help="TSV file without header and without row names. This file describes the connections between the blocks. It should contain 1 (if two blocks are related) or 0 values otherwise. The columns are separated by tabulations. It is a symmetric matrix with the same dimension as the number of blocks."/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	131
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	132 <param name="superblock" type="boolean" truevalue="" falsevalue="--superblock" checked="true" label="Use a superblock"
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	133 help="A block defined as the concatenation of all the other blocks. The space spanned by global components is viewed as a compromise space that integrated all the modalities and facilitates the visualization of the results and their interpretation. If disabled, all blocks are assumed to be connected or a connection file could be used."/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	134
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	135 <conditional name="supervised">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	136 <param name="learning_mode" type="select" display="radio" label="Learning mode">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	137 <option value="unsupervised">Unsupervised</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	138 <option value="supervised">Supervised</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	139 </param>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	140 <when value="supervised">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	141 <param name="block_response" type="integer" value="1" min="1" max="10" label="Use a block as response (supervised analysis)" help="@BLOCK_RULES@ By default, the first block is selected."/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	142 </when>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	143 <when value="unsupervised"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	144 </conditional>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	145
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	146 <conditional name="tau">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	147 <param name="bool" type="select" display="radio" label="Tau selection"
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	148 help="For RGCCA, a regularization parameter for each block (i.e., tau) [default: 1]. Tau varies from 0 (maximizing the correlation) to 1 (maximizing the covariance). For SGCCA, tau is automatically set to 1 and a shrinkage parameter can be defined instead for automatic variable selection, varying from the square root of the variable number (the fewest selected variables) to 1 (all the variables are included).">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	149 <option value="false">Manual</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	150 <option value="optimal">Optimal</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	151 </param>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	152 <when value="false">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	153 <param name="value" type="float" label=" " value="1" min="0" max="1"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	154 </when>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	155 <when value="optimal"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	156 </conditional>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	157
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	158 <param name="scheme" type="select" label="Scheme function" help="Link (i.e. scheme) function for covariance maximization is calculated with: the identity function (horst scheme),
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	159 the absolute values (centroid scheme), the squared values (factorial scheme). Only, the horst scheme penalizes structural
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	160 negative correlation. The factorial scheme discriminates more strongly the blocks than the centroid one.">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	161 <option value="1">Horst : f(x)</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	162 <option value="2" selected="true">Factorial : f(x)^2</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	163 <option value="3">Centroid : f\|x\|</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	164 <option value="4">Other: f(x)^4</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	165 </param>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	166
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	167 </section>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	168
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	169 <section name="graphic" title="Advanced graphic" help="By default, the x-axis and y-axis are respectively the first and the second components, the number of top variables is 100 and a superblock is used.">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	170 <param name="response" optional="true" type="data" format="tsv,tabular,txt,csv" label="Color the individual plot with a response variable"
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	171 help="A TSV file containing either: (i) an only column with a qualitative or a quantitative variable; (ii) multiple columns corresponding to a disjunctive table."/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	172 <param name="text" type="boolean" truevalue="" falsevalue="--text" checked="true" label="Display the names of the points (in biplots)"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	173 <param name="compx" type="integer" label="Component for the X-axis" help="The component used in the X-axis for biplots and the only component used for top variable plot. @COMP_RULES@" value="1" min="1" max="5"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	174 <param name="compy" type="integer" label="Component for the Y-axis" help="The component used in the Y-axis for biplots. @COMP_RULES@" value="2" min="1" max="5"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	175 <param name="blockx" type="integer" value="0" min="0" max="10" label="Visualise this block" help="Block used in the X-axis for individual plot and the only block used for corcircle and top variable plots. @BLOCK_RULES@"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	176 <param name="blocky" type="integer" value="0" min="0" max="10" label="Visualise this block for the Y-axis (in individual plot)" help="0 corresponds to the superblock (or the last block loaded), @BLOCK_RULES@ By default, the superblock is selected."/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	177 <param name="nmark" type="integer" label="Number of top variables" value="100" min="10" max="300"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	178 </section>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	179
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	180 <param name="output_selector" type="select" multiple="true" label="Outputs">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	181 <option value="individuals" selected="true">Individual plot</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	182 <option value="corcircle" selected = "true">Corcircle plot</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	183 <option value="top_variables">Top variables plot</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	184 <option value="ave">Averages plot</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	185 <option value="design">Design plot</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	186 <option value="individual_table" selected="true">Individual table</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	187 <option value="variable_table" selected="true">Variable table</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	188 <option value="rdata">RData file</option>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	189 </param>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	190 </inputs>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	191
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	192 <outputs>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	193 <data name="individual_plot" label="${tool.name} on ${on_string}: individuals.pdf" format="pdf">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	194 <filter>"individuals" in output_selector</filter>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	195 </data>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	196 <data name="corcircle" label="${tool.name} on ${on_string}: corcircle.pdf" format="pdf">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	197 <filter>"corcircle" in output_selector</filter>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	198 </data>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	199 <data name="top_variables" label="${tool.name} on ${on_string}: top_variables.pdf" format="pdf">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	200 <filter>"top_variables" in output_selector</filter>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	201 </data>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	202 <data name="ave" label="${tool.name} on ${on_string}: ave.pdf" format="pdf">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	203 <filter>"ave" in output_selector</filter>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	204 </data>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	205 <data name="design" label="${tool.name} on ${on_string}: design.pdf" format="pdf">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	206 <filter>"design" in output_selector</filter>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	207 </data>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	208 <data name="individual_table" label="${tool.name} on ${on_string}: individuals.tsv" format="tsv">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	209 <filter>"individual_table" in output_selector</filter>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	210 </data>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	211 <data name="variable_table" label="${tool.name} on ${on_string}: variables.tsv" format="tsv">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	212 <filter>"variable_table" in output_selector</filter>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	213 </data>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	214 <data name="rdata" label="${tool.name} on ${on_string}: rgcca.result.RData" format="rdata">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	215 <filter>"rdata" in output_selector</filter>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	216 </data>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	217 </outputs>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	218
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	219 <tests>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	220
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	221 <test expect_num_outputs="8" expect_exit_code="0">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	222 <expand macro="output_tests" path="1block"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	223 <param name="blocks" value="agriculture.tsv" ftype = "tsv"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	224 <output name="individual_table">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	225 <assert_contents>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	226 <has_n_columns n="4"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	227 <has_line_matching
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	228 expression='"agriculture.axis1"\s"agriculture.axis2"\s"superblock.axis1"\s"superblock.axis2"'/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	229 <has_line_matching
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	230 expression='^.+(\s\-?\d+.\d+){4}$'/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	231 </assert_contents>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	232 </output>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	233 </test>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	234
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	235 <test expect_num_outputs="8" expect_exit_code="0">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	236 <expand macro="output_tests" path="3blocks_connection"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	237 <expand macro="output_tests_3blocks"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	238 <section name="analyse">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	239 <param name="connection" value="connection.tsv" ftype = "tsv"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	240 <param name="superblock" value="false"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	241 </section>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	242 <assert_command>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	243 <has_text text="-connection"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	244 <has_text text="--superblock"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	245 </assert_command>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	246 </test>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	247
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	248 <test expect_num_outputs="8" expect_exit_code="0">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	249 <expand macro="output_tests" path="3blocks_supervised"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	250 <expand macro="output_tests_3blocks"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	251 <section name="analyse">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	252 <param name="superblock" value="false"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	253 <conditional name="supervised" >
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	254 <param name="learning_mode" value="supervised"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	255 <param name="block_response" value="3"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	256 </conditional>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	257 </section>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	258 <assert_command>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	259 <has_text text="--response 3"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	260 <has_text text="--superblock"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	261 </assert_command>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	262 </test>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	263
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	264 <test expect_num_outputs="8" expect_exit_code="0">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	265 <expand macro="output_tests" path="3blocks"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	266 <expand macro="output_tests_3blocks"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	267 </test>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	268
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	269 <test expect_num_outputs="8" expect_exit_code="0">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	270 <expand macro="output_tests" path="3blocks_sgcca"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	271 <expand macro="output_tests_3blocks"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	272 <section name="analyse">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	273 <conditional name="method">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	274 <param name="family" value="m"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	275 <param name="type" value="sgcca"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	276 </conditional>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	277 </section>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	278 <assert_command>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	279 <has_text text="sgcca"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	280 </assert_command>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	281 </test>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	282
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	283 <test expect_num_outputs="8" expect_exit_code="0">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	284 <expand macro="output_tests" path="2blocks" compx="3" compy="1"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	285 <param name="blocks" value="agriculture.tsv,politic.tsv"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	286 <section name="analyse">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	287 <param name="scale" value="false"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	288 <conditional name="tau">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	289 <param name="bool" value="false"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	290 <param name="value" value="0"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	291 </conditional>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	292 <param name="scheme" value="3"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	293 <param name="ncomp" value="3"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	294 <conditional name="method">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	295 <param name="family" value="2"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	296 <param name="type" value="pls"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	297 </conditional>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	298 </section>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	299 <section name="graphic">
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	300 <param name="response" value="political_system.tsv" ftype = "tsv"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	301 <param name="text" value="false"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	302 <param name="compx" value="3"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	303 <param name="compy" value="1"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	304 <param name="blockx" value="2"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	305 <param name="blocky" value="1"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	306 <param name="nmark" value="11"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	307 </section>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	308 <assert_command>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	309 <has_text text="pls"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	310 <has_text text="--group"/>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	311 </assert_command>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	312 </test>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	313
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	314 </tests>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	315 <help>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	316
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	317 ==================================
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	318 ABOUT
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	319 ==================================
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	320
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	321
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	322 Author:
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	323 Etienne CAMENEN
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	324
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	325
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	326 Contact:
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	327 arthur.tenenhaus@centralesupelec.fr
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	328
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	329
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	330 R package:
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	331 The RGCCA package is available from the CRAN repository (https://cran.r-project.org/web/packages/RGCCA).
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	332
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	333 ---------------------------------------------------
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	334
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	335 ==================================
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	336 R/SGCCA
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	337 ==================================
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	338
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	339 A user-friendly multi-blocks analysis (Regularized Generalized Canonical Correlation Analysis, RGCCA) as described in [1] and [2] with all default settings predefined. The software produces figures to explore the analysis' results: individuals and variables projected on two components of the multi-block analysis, list of top variables and explained variance in the model.
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	340
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	341 Working example
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	342
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	343 \| From Russett data (RGCCA package): https://github.com/rgcca-factory/RGCCA/tree/master/inst/extdata
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	344 \| 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.
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	345
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	346 Documentation
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	347
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	348 - RGCCA: https://cran.r-project.org/web/packages/RGCCA/vignettes/vignette_RGCCA.pdf
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	349 - accepted input / output formats: https://github.com/rgcca-factory/RGCCA#input-files
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	350 <!-- - tutorial: https://github.com/BrainAndSpineInstitute/rgcca_galaxy/blob/release/0.2/README.md-->
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	351
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	352 </help>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	353
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	354 <citations>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	355 <citation type="doi">10.1007/s11336-017-9573-x</citation>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	356 <citation type="doi">10.1007/s11336-011-9206-8</citation>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	357 </citations>
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	358
067d45e6caa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771" iuc parents: diff changeset	359 </tool>

Mercurial > repos > iuc > rgcca

annotate rgcca.xml @ 0:067d45e6caa9 draft