Mercurial > repos > iuc > rgcca

annotate rgcca.xml @ 1:6bf48c098d36 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
author iuc
date Sun, 18 Jul 2021 18:02:32 +0000
parents 4809cae1b724
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
1 <tool id="rgcca" name="RGCCA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
2
4809cae1b724 "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>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
4
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
5 <macros>
4809cae1b724 "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>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
7 </macros>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
8
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
9 <edam_topics>
4809cae1b724 "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>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
11 </edam_topics>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
12
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
13 <edam_operations>
4809cae1b724 "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>
4809cae1b724 "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>
4809cae1b724 "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>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
17 </edam_operations>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
18
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
19 <requirements>
4809cae1b724 "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>
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
21 <requirement type="package" version="4.1">r-base</requirement>
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
22 </requirements>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
23
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
24 <command detect_errors="exit_code"><![CDATA[
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
25 #set data_paths = ",".join([str(_.file_name) for _ in $blocks])
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
26 #set data_names = ",".join([str(_.element_identifier).replace(',', '_') for _ in $blocks])
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
27 #set out_files = str($output_selector).split(",")
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
28 Rscript '$__tool_directory__/launcher.R'
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
29 --datasets '${data_paths}'
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
30 --names '${data_names}'
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
31 #if 'individuals' in $out_files
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
32 --o1 '$individual_plot'
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
33 #end if
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
34 #if 'corcircle' in $out_files
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
35 --o2 '$corcircle'
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
36 #end if
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
37 #if 'top_variables' in $out_files
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
38 --o3 '$top_variables'
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
39 #end if
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
40 #if 'ave' in $out_files
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
41 --o4 '$ave'
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
42 #end if
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
43 #if 'design' in $out_files
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
44 --o5 '$design'
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
45 #end if
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
46 #if 'individual_table' in $out_files
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
47 --o6 '$individual_table'
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
48 #end if
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
49 #if 'variable_table' in $out_files
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
50 --o7 '$variable_table'
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
51 #end if
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
52 #if 'rdata' in $out_files
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
53 --o8 '$rdata'
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
54 #end if
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
55 $parse.header
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
56 --separator $parse.separator
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
57 $analyse.superblock
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
58 $analyse.scale
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
59 #if $analyse.tau.bool == 'false'
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
60 --penalty $analyse.tau.value
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
61 #else
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
62 --penalty $analyse.tau.bool
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
63 #end if
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
64 --ncomp $analyse.ncomp
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
65 --scheme $analyse.scheme
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
66 #if $analyse.method.family == '1'
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
67 --type pca
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
68 #else
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
69 --type $analyse.method.type
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
70 #end if
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
71 #if $analyse.connection
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
72 --connection $analyse.connection
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
73 #end if
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
74 #if $analyse.supervised.learning_mode == 'supervised'
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
75 --response $analyse.supervised.block_response
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
76 #end if
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
77 #if $graphic.response
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
78 --group $graphic.response
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
79 #end if
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
80 --compx $graphic.compx
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
81 --compy $graphic.compy
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
82 --nmark $graphic.nmark
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
83 $graphic.text
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
84 --block $graphic.blockx
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
85 --block_y $graphic.blocky
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
86 ]]></command>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
87
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
88 <inputs>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
89 <param name="blocks" type="data" format="tsv,tabular,txt,csv" multiple="true" optional="false" label = "Load blocks"
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
90 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)."/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
91
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
92 <section name="parse" title="Advanced parsing" help="By default, on tabulated files with a header.">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
93 <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."/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
94 <param name="separator" type="select" display="radio" label="Column separator" help="Character used to separate the column (for all blocks, connection and color files).">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
95 <option value="1" selected="true">Tabulation</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
96 <option value="2">Semicolon</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
97 </param>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
98 </section>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
99
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
100 <section name="analyse" title="Advanced analysis"
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
101 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.">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
102
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
103 <param name="ncomp" type="integer" label="Number of component" value="2" min="2" max="5"
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
104 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)."/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
105
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
106 <param name="scale" type="boolean" truevalue="" falsevalue="--scale" checked="true" label="Scale the blocks"
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
107 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."/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
108
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
109 <conditional name="method">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
110
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
111 <param name="family" type="select" label="Analysis method">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
112 <option value="1">One block</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
113 <option value="2">Two blocks</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
114 <option value="m" selected="true">Multiple blocks</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
115 <option value="ms">Multiple blocks with superblock</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
116 </param>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
117
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
118 <when value="2">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
119 <param name="type" type="select" label=" ">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
120 <option value="pls">Partial Least Squares Regression</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
121 <option value="cca">Canonical Correlation Analysis</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
122 <option value="ifa">Interbattery Factor Analysis</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
123 <option value="ra">Redundancy analysis</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
124 </param>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
125 </when>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
126
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
127 <when value="m">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
128 <param name="type" type="select" label=" ">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
129 <option value="rgcca">Regularized Generalized CCA</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
130 <option value="sgcca">Sparse Generalized CCA</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
131 <option value="sumcor">SUM of CORrelations method</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
132 <option value="ssqcor">Sum of SQuared CORrelations method</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
133 <option value="sabscor">Sum of ABSolute value CORrelations method</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
134 <option value="sumcov">SUM of COVariances method</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
135 <option value="ssqcov">Sum of SQuared COVariances method</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
136 <option value="sabscov">Sum of ABSolute value COVariances method</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
137 <option value="maxbet">MAXBET</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
138 <option value="maxbet-b">MAXBET-B</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
139 </param>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
140 </when>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
141
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
142 <when value="ms">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
143 <param name="type" type="select" label=" ">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
144 <option value="gcca">Generalized CCA</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
145 <option value="hpca">Hierarchical PCA</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
146 <option value="mfa">Multiple Factor Analysis</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
147 </param>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
148 </when>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
149
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
150 <when value="1"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
151
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
152 </conditional>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
153
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
154 <param name="connection" optional="true" type="data" format="tsv,tabular,txt,csv" label="Load the design matrix (if superblock or supervised disabled)"
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
155 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."/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
156
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
157 <param name="superblock" type="boolean" truevalue="" falsevalue="--superblock" checked="true" label="Use a superblock"
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
158 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."/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
159
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
160 <conditional name="supervised">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
161 <param name="learning_mode" type="select" display="radio" label="Learning mode">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
162 <option value="unsupervised">Unsupervised</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
163 <option value="supervised">Supervised</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
164 </param>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
165 <when value="supervised">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
166 <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."/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
167 </when>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
168 <when value="unsupervised"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
169 </conditional>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
170
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
171 <conditional name="tau">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
172 <param name="bool" type="select" display="radio" label="Tau selection"
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
173 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).">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
174 <option value="false">Manual</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
175 <option value="optimal">Optimal</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
176 </param>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
177 <when value="false">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
178 <param name="value" type="float" label=" " value="1" min="0" max="1"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
179 </when>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
180 <when value="optimal"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
181 </conditional>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
182
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
183 <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),
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
184 the absolute values (centroid scheme), the squared values (factorial scheme). Only, the horst scheme penalizes structural
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
185 negative correlation. The factorial scheme discriminates more strongly the blocks than the centroid one.">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
186 <option value="1">Horst : f(x)</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
187 <option value="2" selected="true">Factorial : f(x)^2</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
188 <option value="3">Centroid : f|x|</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
189 <option value="4">Other: f(x)^4</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
190 </param>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
191
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
192 </section>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
193
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
194 <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.">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
195 <param name="response" optional="true" type="data" format="tsv,tabular,txt,csv" label="Color the individual plot with a response variable"
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
196 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."/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
197 <param name="text" type="boolean" truevalue="" falsevalue="--text" checked="true" label="Display the names of the points (in biplots)"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
198 <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"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
199 <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"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
200 <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@"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
201 <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."/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
202 <param name="nmark" type="integer" label="Number of top variables" value="100" min="10" max="300"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
203 </section>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
204
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
205 <param name="output_selector" type="select" multiple="true" label="Outputs">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
206 <option value="individuals" selected="true">Individual plot</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
207 <option value="corcircle" selected = "true">Corcircle plot</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
208 <option value="top_variables">Top variables plot</option>
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
209 <option value="ave">Explained variance plot</option>
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
210 <option value="design">Design plot</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
211 <option value="individual_table" selected="true">Individual table</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
212 <option value="variable_table" selected="true">Variable table</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
213 <option value="rdata">RData file</option>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
214 </param>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
215 </inputs>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
216
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
217 <outputs>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
218 <data name="individual_plot" label="${tool.name} on ${on_string}: individuals.pdf" format="pdf">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
219 <filter>"individuals" in output_selector</filter>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
220 </data>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
221 <data name="corcircle" label="${tool.name} on ${on_string}: corcircle.pdf" format="pdf">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
222 <filter>"corcircle" in output_selector</filter>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
223 </data>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
224 <data name="top_variables" label="${tool.name} on ${on_string}: top_variables.pdf" format="pdf">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
225 <filter>"top_variables" in output_selector</filter>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
226 </data>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
227 <data name="ave" label="${tool.name} on ${on_string}: ave.pdf" format="pdf">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
228 <filter>"ave" in output_selector</filter>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
229 </data>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
230 <data name="design" label="${tool.name} on ${on_string}: design.pdf" format="pdf">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
231 <filter>"design" in output_selector</filter>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
232 </data>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
233 <data name="individual_table" label="${tool.name} on ${on_string}: individuals.tsv" format="tsv">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
234 <filter>"individual_table" in output_selector</filter>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
235 </data>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
236 <data name="variable_table" label="${tool.name} on ${on_string}: variables.tsv" format="tsv">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
237 <filter>"variable_table" in output_selector</filter>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
238 </data>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
239 <data name="rdata" label="${tool.name} on ${on_string}: rgcca.result.RData" format="rdata">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
240 <filter>"rdata" in output_selector</filter>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
241 </data>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
242 </outputs>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
243
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
244 <tests>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
245
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
246 <test expect_num_outputs="8" expect_exit_code="0">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
247 <expand macro="output_tests" path="1block"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
248 <param name="blocks" value="agriculture.tsv" ftype = "tsv"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
249 <output name="individual_table">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
250 <assert_contents>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
251 <has_n_columns n="4"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
252 <has_line_matching
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
253 expression='"agriculture.component1"\s"agriculture.component2"\s"superblock.component1"\s"superblock.component2"'/>
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
254 <has_line_matching
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
255 expression='^.+(\s\-?\d+.\d+){4}$'/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
256 </assert_contents>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
257 </output>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
258 </test>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
259
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
260 <test expect_num_outputs="8" expect_exit_code="0">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
261 <expand macro="output_tests" path="3blocks_connection"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
262 <expand macro="output_tests_3blocks"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
263 <section name="analyse">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
264 <param name="connection" value="connection.tsv" ftype = "tsv"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
265 <param name="superblock" value="false"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
266 </section>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
267 <assert_command>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
268 <has_text text="-connection"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
269 <has_text text="--superblock"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
270 </assert_command>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
271 </test>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
272
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
273 <test expect_num_outputs="8" expect_exit_code="0">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
274 <expand macro="output_tests" path="3blocks_supervised"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
275 <expand macro="output_tests_3blocks"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
276 <section name="analyse">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
277 <param name="superblock" value="false"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
278 <conditional name="supervised" >
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
279 <param name="learning_mode" value="supervised"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
280 <param name="block_response" value="3"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
281 </conditional>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
282 </section>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
283 <assert_command>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
284 <has_text text="--response 3"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
285 <has_text text="--superblock"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
286 </assert_command>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
287 </test>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
288
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
289 <test expect_num_outputs="8" expect_exit_code="0">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
290 <expand macro="output_tests" path="3blocks"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
291 <expand macro="output_tests_3blocks"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
292 </test>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
293
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
294 <test expect_num_outputs="8" expect_exit_code="0">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
295 <expand macro="output_tests" path="3blocks_sgcca"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
296 <expand macro="output_tests_3blocks"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
297 <section name="analyse">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
298 <conditional name="method">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
299 <param name="family" value="m"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
300 <param name="type" value="sgcca"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
301 </conditional>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
302 </section>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
303 <assert_command>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
304 <has_text text="sgcca"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
305 </assert_command>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
306 </test>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
307
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
308 <test expect_num_outputs="8" expect_exit_code="0">
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
309 <expand macro="output_tests" path="2blocks"/>
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
310 <param name="blocks" value="agriculture.tsv,politic.tsv"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
311 <section name="analyse">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
312 <param name="scale" value="false"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
313 <conditional name="tau">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
314 <param name="bool" value="false"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
315 <param name="value" value="0"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
316 </conditional>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
317 <param name="scheme" value="3"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
318 <param name="ncomp" value="3"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
319 <conditional name="method">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
320 <param name="family" value="2"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
321 <param name="type" value="pls"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
322 </conditional>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
323 </section>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
324 <section name="graphic">
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
325 <param name="response" value="political_system.tsv" ftype = "tsv"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
326 <param name="text" value="false"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
327 <param name="compx" value="3"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
328 <param name="compy" value="1"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
329 <param name="blockx" value="2"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
330 <param name="blocky" value="1"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
331 <param name="nmark" value="11"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
332 </section>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
333 <assert_command>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
334 <has_text text="pls"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
335 <has_text text="--group"/>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
336 </assert_command>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
337 </test>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
338
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
339 </tests>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
340 <help>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
341
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
342 ==================================
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
343 ABOUT
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
344 ==================================
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
345
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
346
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
347 **Author:**
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
348 Etienne CAMENEN
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
349
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
350
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
351 **Contact:**
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
352 etienne.camenen@gmail.com
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
353
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
354
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
355 **R package:**
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
356 | The RGCCA package is available from the CRAN repository (v2.1.2; https://cran.r-project.org/web/packages/RGCCA).
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
357 | This tool is based on a version available on github (v3.0; https://github.com/rgcca-factory/RGCCA).
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
358
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
359 ---------------------------------------------------
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
360
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
361 ==================================
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
362 R/SGCCA
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
363 ==================================
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
364
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
365 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.
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
366
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
367 **Working example**
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
368
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
369 | From Russett data (RGCCA package): https://github.com/BrainAndSpineInstitute/rgcca_ui/tree/master/inst/extdata
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
370 | 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.
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
371
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
372 **Documentation**
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
373
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
374 - RGCCA: https://cran.r-project.org/web/packages/RGCCA/vignettes/vignette_RGCCA.pdf
1
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
375 - accepted input / https://github.com/BrainAndSpineInstitute/rgcca_ui#input-files
6bf48c098d36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit ce05b5eb018ae1c4d580ab5ce1a33896c1aa8c5b"
iuc
parents: 0
diff changeset
376 - tutorial: https://github.com/BrainAndSpineInstitute/rgcca_galaxy#readme
0
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
377
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
378 </help>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
379
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
380 <citations>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
381 <citation type="doi">10.1007/s11336-017-9573-x</citation>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
382 <citation type="doi">10.1007/s11336-011-9206-8</citation>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
383 </citations>
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
384
4809cae1b724 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca commit 00f9e92845737e05a4afb1c93043f35b7e4ea771"
iuc
parents:
diff changeset
385 </tool>