Mercurial > repos > ppericard > mixomics_blocksplsda
annotate mixomics_blocksplsda.xml @ 4:b0ab97ffc2a1 draft
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
author | ppericard |
---|---|
date | Mon, 09 Mar 2020 11:53:32 -0400 |
parents | 6595c17673cb |
children | 1ee8d2c20c0a |
rev | line source |
---|---|
4
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.3.0" profile="16.04" workflow_compatible="true"> |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
2 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
3 <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description> |
4
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
4 |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
5 <requirements> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
7 <requirement type="package" version="2.0">r-argparse</requirement> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
8 </requirements> |
4
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
9 |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
10 <!-- <stdio> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
11 <exit_code range="1:" level="fatal" /> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
12 </stdio> --> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
13 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
14 <command detect_errors="aggressive"> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
15 <![CDATA[ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
16 mkdir outdir |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
17 && Rscript |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
18 ${__tool_directory__}/mixomics_blocksplsda_script.R |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
19 #for $b in $blocks |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
20 --block |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
21 #if $b.block_name |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
22 ${b.block_name} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
23 #else |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
24 ${b.data_matrix.name} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
25 #end if |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
26 ${b.keep} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
27 ${b.data_matrix} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
28 ${b.variable_metadata} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
29 #end for |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
30 --sample_metadata_in ${sample_metadata_in} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
31 --sample_description_col ${sample_description_col} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
32 --ncomp ${ncomp} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
33 ${correlation} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
34 --scheme ${adv.scheme} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
35 --mode ${adv.mode} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
36 --maxiter ${adv.maxiter} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
37 ${adv.scale} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
38 --init ${adv.init} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
39 --tol ${adv.tol} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
40 ${adv.nearzerovar} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
41 --rdata_out ${rdata_out} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
42 --sample_metadata_out ${sample_metadata_out} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
43 --variable_metadata_outdir outdir |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
44 ]]> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
45 </command> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
46 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
47 <inputs> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
48 <repeat name="blocks" title="Blocks"> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
49 <param name="block_name" type="text" label="Block name" /> |
4
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
50 <param name="keep" type="integer" value="0" min="0" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
51 label="Number of variables to select for each component" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
52 help="[keep] Estimation of the number of variables in the block correlated with variables from the other blocks and correlated with response variables. If set to 0, all variables will be selected." /> |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
53 <param name="data_matrix" type="data" format="tabular" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
54 label="Data matrix" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
55 help="Block data in tabular format (rows = variables, columns = samples). The first column contains the variables names and the first row contains the samples names. Samples names must be in the same order for all blocks and the sample metadata (transposed). The data must not contain missing values." /> |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
56 <param name="variable_metadata" type="data" format="tabular" optional="true" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
57 label="Variables metadata [optional]" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
58 help="Variables metadata in tabular format (rows = variables). The first colum contains the variables names. The first row contains the metadata column names. The number of rows in the metadata file must be the same than the number of rows in the block data file, and the variables need to be in the same order. If a metadata file is provided, block.splsda output will be appended as new columns, otherwise a new file will be created." /> |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
59 </repeat> |
4
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
60 <param name="sample_metadata_in" type="data" format="tabular" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
61 label="Samples metadata" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
62 help="Samples metadata in tabular format (rows = samples). The first column contains the sample names. The first row contains the metadata column names. Samples names must be in the same order (transposed) than all the blocks. One of the column (the last by default) must contain the samples groups for integration." /> |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
63 <param name="sample_description_col" type="integer" value="0" min="0" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
64 label="Samples groups column number" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
65 help="Column from the samples metadata file containing samples groups. If set to 0, the last column will be used." /> |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
66 <param name="ncomp" type="integer" value="2" min="1" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
67 label="Number of components to include in the model" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
68 help="[ncomp] Number of new variables (components) computed by the data integration." /> |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
69 <param name="correlation" type="boolean" truevalue="--correlation" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
70 falsevalue="" checked="false" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
71 label="Correlation between all blocks" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
72 help="[design] If set to Yes, data integration will take into account correlations between all the blocks (design matrix with diagonal coefficients set to 0 and the rest of the coefficients set to 1)." /> |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
73 <section name="adv" title="Advanced Options" expanded="false"> |
4
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
74 <!-- <param name="scheme" type="select" label="Scheme"> |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
75 <option value="horst" selected="true">horst</option> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
76 <option value="factorial" >factorial</option> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
77 <option value="centroid" >centroid</option> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
78 </param> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
79 <param name="mode" type="select" label="Mode"> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
80 <option value="regression" selected="true">regression</option> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
81 <option value="canonical" >canonical</option> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
82 <option value="invariant" >invariant</option> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
83 <option value="classic" >classic</option> |
4
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
84 </param> --> |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
85 <param name="maxiter" type="integer" value="100" min="1" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
86 label="Maximum number of iterations" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
87 help="[max.iter] Maximum number of iterations performed by block.splsda." /> |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
88 <!-- <param name="scale" type="boolean" truevalue="-\-scale" falsevalue="" checked="true" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
89 label="Scale" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
90 help="if checked, each block is standardized to zero means and unit variances" /> |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
91 <param name="init" type="select" label="Init"> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
92 <option value="svd" selected="true">svd</option> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
93 <option value="svd.single" >svd.single</option> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
94 </param> |
4
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
95 <param name="tol" type="float" value="1e-06" min="0" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
96 label="Convergence stopping value" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
97 help="[tol]" /> |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
98 <param name="nearzerovar" type="boolean" truevalue="-\-nearzerovar" falsevalue="" checked="false" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
99 label="Should be set to TRUE in particular for data with many zero values" /> --> |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
100 </section> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
101 </inputs> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
102 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
103 <outputs> |
1
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
104 <data name="rdata_out" format="rdata" label="${tool.name}_output.rdata" /> |
4
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
105 <data name="sample_metadata_out" format="tabular" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
106 label="${tool.name}_${sample_metadata_in.name}" /> |
1
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
107 <collection name="blocks_output" type="list" label="${tool.name}_blocks_output"> |
4
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
108 <discover_datasets pattern="(?P<designation>.+)\.tsv" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents:
1
diff
changeset
|
109 directory="outdir" format="tabular" /> |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
110 </collection> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
111 </outputs> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
112 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
113 <tests> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
114 <test> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
115 <repeat name="blocks"> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
116 <param name="block_name" value="Block1" /> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
117 <param name="data_matrix" value="in_block1_data.tabular" /> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
118 </repeat> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
119 <repeat name="blocks"> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
120 <param name="block_name" value="Block2" /> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
121 <param name="data_matrix" value="in_block2_data.tabular" /> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
122 </repeat> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
123 <param name="sample_metadata_in" value="in_sample_meta.tabular" /> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
124 <output name="rdata_out" value="out_rdata.rdata" /> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
125 <output name="sample_metadata_out" value="out_sample_meta.tabular" /> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
126 </test> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
127 </tests> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
128 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
129 <help> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
130 <![CDATA[ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
131 .. class:: infomark |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
132 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
133 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr) |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
134 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
135 --------------------------------------------------- |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
136 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
137 .. class:: infomark |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
138 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
139 **Please cite** |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
140 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
141 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration. |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
142 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
143 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
144 --------------------------------------------------- |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
145 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
146 ====================== |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
147 mixOmics blocks.splsda |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
148 ====================== |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
149 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
150 ----------- |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
151 Description |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
152 ----------- |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
153 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
154 The blocks.splsda function is part of the mixOmics package for exploration and integration of Omics datasets. |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
155 Performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis. |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
156 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
157 ----------- |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
158 Input files |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
159 ----------- |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
160 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
161 For each block (min 2 blocks): |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
162 ============================== |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
163 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
164 +------------------------------+------------+ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
165 | Parameter : num + label | Format | |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
166 +==============================+============+ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
167 | 1 : Data matrix | tabular | |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
168 +------------------------------+------------+ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
169 | 2 : [opt] Variables metadata | tabular | |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
170 +------------------------------+------------+ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
171 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
172 Variables metadata files are optional. |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
173 If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created. |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
174 |
1
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
175 1. Data matrix format |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
176 * Rows = variables, Columns = samples |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
177 * First row = samples name. MUST be the same and in the same order in every block as well as in the sample metadata file (transposed) |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
178 * First column = variables name |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
179 |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
180 2. Variables metadata format |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
181 * Rows = variables, Columns = metadata |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
182 * First row = metadata column names |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
183 * First column = variables names. MUST be the same and in the same order than in the associated data matrix |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
184 |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
185 Global input files: |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
186 =================== |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
187 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
188 +-----------------------------+------------+ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
189 | Parameter : num + label | Format | |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
190 +=============================+============+ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
191 | 1 : Samples metadata | tabular | |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
192 +-----------------------------+------------+ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
193 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
194 By default, the last column of the samples metadata matrix will be used as samples description factors. |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
195 If it's not the case, the column number can be inputed in the `Sample description column number` parameter. |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
196 |
1
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
197 1. Samples metadata format |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
198 * Rows = samples, Columns = metadata |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
199 * First row = metadata column names |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
200 * First column = sample names. These names must be identical (transposed) and in the same order than for the blocks data matrices |
6595c17673cb
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
ppericard
parents:
0
diff
changeset
|
201 |
0
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
202 ---------- |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
203 Parameters |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
204 ---------- |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
205 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
206 For each block (min 2 blocks): |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
207 ============================== |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
208 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
209 Block name |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
210 Name of the block. If not provided, this will default to the input filename |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
211 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
212 Number of variables to select for each component |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
213 If set to 0 (default), all variables will be considered in the model |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
214 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
215 Global parameters: |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
216 ================== |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
217 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
218 Sample description column number |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
219 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
220 Number of components to include in the model |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
221 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
222 Correlation between all blocks |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
223 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
224 Advanced options: |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
225 ================= |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
226 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
227 Scheme |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
228 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
229 Mode |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
230 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
231 Maximum number of iterations |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
232 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
233 Scale |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
234 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
235 Init |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
236 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
237 Convergence stopping value (tol) |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
238 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
239 Near zero var |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
240 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
241 ------------ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
242 Output files |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
243 ------------ |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
244 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
245 mixomics_blocksplsda_output.rdata |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
246 | rData output |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
247 | Contains the `mixomics_result` R object containing the result of the block.splsda function |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
248 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
249 mixomics_blocksplsda_{input_sample_metadata_name} |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
250 | tabular output |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
251 | Identical to the input Sample metadata file with appended columns from the result of block.splsda function |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
252 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
253 mixomics_blocksplsda_blocks_output |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
254 A collection with the variable metadata output files (mixomics_blocksplsda_block_{block name}_variable_metadata) for each input block |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
255 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
256 ]]> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
257 </help> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
258 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
259 <citations> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
260 <citation type="doi">10.1371/journal.pcbi.1005752</citation> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
261 </citations> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
262 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
ppericard
parents:
diff
changeset
|
263 </tool> |