Mercurial > repos > ppericard > viscorvar
annotate mixomics_blocksplsda.xml @ 4:d4e9f7546dfa draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
author | ppericard |
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date | Tue, 17 Nov 2020 13:01:44 +0000 |
parents | c8533e9298e5 |
children | 88c1fd2ac110 |
rev | line source |
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4
d4e9f7546dfa
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
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1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true"> |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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2 |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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3 <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description> |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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4 |
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5 <macros> |
c8533e9298e5
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6 <import>macros.xml</import> |
c8533e9298e5
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7 <import>macros_mixomics.xml</import> |
c8533e9298e5
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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8 </macros> |
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9 |
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10 <expand macro="requirements"/> |
c8533e9298e5
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11 <expand macro="stdio"/> |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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12 |
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13 <command detect_errors="aggressive"><![CDATA[ |
c8533e9298e5
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14 |
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15 mkdir outdir |
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16 && @COMMAND_RSCRIPT@/mixomics_blocksplsda.R |
c8533e9298e5
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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17 |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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18 #for $b in $blocks |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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19 --block |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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20 #if $b.block_name |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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21 ${b.block_name} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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22 #else |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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23 ${b.data_matrix.name} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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24 #end if |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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25 ${b.keep} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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26 ${b.data_matrix} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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27 ${b.variable_metadata} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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28 #end for |
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29 |
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30 --sample_metadata_in ${sample_metadata_in} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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31 --sample_description_col ${sample_description_col} |
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32 |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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33 --ncomp ${adv.ncomp} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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34 ${correlation} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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35 ##--scheme ${adv.scheme} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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36 ##--mode ${adv.mode} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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37 --maxiter ${adv.maxiter} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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38 ##${adv.scale} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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39 --scale ## always activated hidden param |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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40 ${adv.check_missing_values} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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41 ##--init ${adv.init} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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42 ##--tol ${adv.tol} |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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43 ##${adv.nearzerovar} |
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44 |
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45 --rdata_out ${rdata_out} |
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46 ##--sample_metadata_out ${sample_metadata_out} |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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47 --variable_metadata_outdir outdir |
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48 |
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49 ]]></command> |
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50 |
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51 <inputs> |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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52 <repeat name="blocks" title="Blocks"> |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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53 <param name="block_name" type="text" label="Block name" /> |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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54 <param name="keep" type="integer" value="0" min="0" |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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55 label="Number of variables to select for each component" |
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56 help="estimation of the number of variables of the block correlated with variables of the other blocks and correlated with response variables. If set to 0, all variables will be selected" /> |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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57 <param name="data_matrix" type="data" format="tabular" |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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58 label="Data matrix" |
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59 help="data matrix contains the values of the variables. For the file structure, see below in the section Input files" /> |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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60 <param name="variable_metadata" type="data" format="tabular" optional="true" |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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61 label="Variables metadata [optional]" |
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62 help="variables metadata contains the metadata of the variables. For the file structure, see below in the section Input files" /> |
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63 </repeat> |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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64 <param name="sample_metadata_in" type="data" format="tabular" |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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65 label="Samples metadata" |
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66 help="samples metadata contains the metadata of the samples. For the file structure, see below in the section Global input files" /> |
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67 <param name="sample_description_col" type="integer" value="0" min="0" |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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68 label="Samples groups column number" |
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69 help="column from the samples metadata file containing samples groups. If set to 0, the last column will be used" /> |
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70 <param name="correlation" type="boolean" truevalue="--correlation" |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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71 falsevalue="" checked="false" |
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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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72 label="Correlation between all blocks" |
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73 help="if set to Yes, data integration will take into account correlations between all the blocks. If set to No, data integration will only take into account correlations between the blocks and the response" /> |
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74 <section name="adv" title="Advanced Options" expanded="false"> |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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75 <param name="ncomp" type="integer" value="2" min="1" |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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76 label="Number of components to include in the model" |
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77 help="number of new variables (components) computed by the data integration" /> |
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78 <!-- <param name="scheme" type="select" label="Scheme"> |
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79 <option value="horst" selected="true">horst</option> |
d0b77b926863
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
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80 <option value="factorial" >factorial</option> |
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81 <option value="centroid" >centroid</option> |
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82 </param> |
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83 <param name="mode" type="select" label="Mode"> |
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84 <option value="regression" selected="true">regression</option> |
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85 <option value="canonical" >canonical</option> |
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86 <option value="invariant" >invariant</option> |
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87 <option value="classic" >classic</option> |
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88 </param> --> |
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89 <param name="maxiter" type="integer" value="100" min="1" |
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90 label="Maximum number of iterations" |
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91 help="maximum number of iterations performed by block.splsda" /> |
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92 <!-- <param name="scale" type="boolean" truevalue="-\-scale" falsevalue="" checked="true" |
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93 label="Scale" |
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94 help="if checked, each block is standardized to zero means and unit variances" /> --> |
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95 <param name="check_missing_values" type="boolean" truevalue="-\-check_missing_values" falsevalue="" checked="true" |
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96 label="Check for missing values" |
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97 help="will raise an error if missing values are found in data matrices" /> |
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98 <!-- <param name="init" type="select" label="Init"> |
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99 <option value="svd" selected="true">svd</option> |
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100 <option value="svd.single" >svd.single</option> |
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101 </param> |
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102 <param name="tol" type="float" value="1e-06" min="0" |
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103 label="Convergence stopping value" |
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104 help="[tol]" /> |
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105 <param name="nearzerovar" type="boolean" truevalue="-\-nearzerovar" falsevalue="" checked="true" |
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106 label="Should be set to TRUE in particular for data with many zero values" /> --> |
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107 </section> |
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108 </inputs> |
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109 |
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110 <outputs> |
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111 <data name="rdata_out" format="rdata" label="${tool.name}_output.RData" /> |
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112 <!-- <data name="sample_metadata_out" format="tabular" |
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113 label="${tool.name}_${sample_metadata_in.name}" /> --> |
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114 <collection name="blocks_output" type="list" label="${tool.name}_blocks_output"> |
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115 <discover_datasets pattern="(?P<designation>.+)\.tsv" |
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116 directory="outdir" format="tabular" /> |
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117 </collection> |
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118 </outputs> |
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119 |
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120 <tests> |
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121 <test> |
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122 <repeat name="blocks"> |
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123 <param name="block_name" value="Block1" /> |
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124 <param name="data_matrix" value="in_block1_data.tabular" /> |
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125 </repeat> |
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126 <repeat name="blocks"> |
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127 <param name="block_name" value="Block2" /> |
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128 <param name="data_matrix" value="in_block2_data.tabular" /> |
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129 </repeat> |
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130 <param name="sample_metadata_in" value="in_sample_meta.tabular" /> |
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131 <!-- <param name="correlation" value=true /> --> |
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132 <output name="rdata_out" value="mixomics_blocksplsda_output.rdata" /> |
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133 <!-- <output name="sample_metadata_out" value="out_sample_meta.tabular" /> --> |
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134 </test> |
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135 </tests> |
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136 |
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137 <help><![CDATA[ |
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138 |
2
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139 @HELP_AUTHORS@ |
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140 |
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141 ====================== |
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142 mixOmics blocks.splsda |
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143 ====================== |
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144 |
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145 ----------- |
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146 Description |
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147 ----------- |
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148 |
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149 The blocks.splsda function is part of the mixOmics package for exploration and integration of omics datasets. |
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150 This data integration takes as input parameters different omics datasets |
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151 (transcriptomic, metabolomic, metagenomic, ...) and a response variable (e.g. for a sample, the value of the response |
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152 variable is equal to « Treated » or « Control »). This data integration returns, for each omics dataset, variables |
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153 which are correlated with the variables of the other omic datasets and the response variable. The other functions of |
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154 this pipeline allow visualizing this correlated variables thanks to correlation circles and networks. |
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155 |
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156 ----------------- |
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157 Workflow position |
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158 ----------------- |
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159 |
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160 **Downstream tools** |
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161 |
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162 ======================= ================================== ========== |
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163 Name Output file Format |
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164 ======================= ================================== ========== |
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165 mixOmics.plotIndiv mixomics_blocksplsda_output.RData rdata |
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166 ----------------------- ---------------------------------- ---------- |
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167 mixOmics.plotVar mixomics_blocksplsda_output.RData rdata |
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168 ----------------------- ---------------------------------- ---------- |
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169 visCorVar.matCorAddVar mixomics_blocksplsda_output.RData rdata |
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170 ======================= ================================== ========== |
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171 |
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172 --------------------------------------------------- |
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173 |
0
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174 ----------- |
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175 Input files |
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176 ----------- |
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177 |
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178 For each block (min 2 blocks): |
2
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179 ------------------------------ |
0
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180 |
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181 +------------------------------+------------+ |
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182 | Parameter : num + label | Format | |
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183 +==============================+============+ |
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184 | 1 : Data matrix | tabular | |
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185 +------------------------------+------------+ |
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186 | 2 : [opt] Variables metadata | tabular | |
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187 +------------------------------+------------+ |
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188 |
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189 1. Data matrix structure |
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190 The data matrix is in tabular format (.tsv). |
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191 The first column contains the variables names. |
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192 The first row contains the samples names. |
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193 Samples names must be in the same order for all blocks and the sample metadata (transposed). The data must not contain missing values. |
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194 |
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195 2. Variables metadata structure |
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196 The variables metadata is in tabular format (.tsv). |
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197 The first colum contains the variables names. |
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198 The first row contains the metadata column names. |
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199 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. |
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200 |
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201 Variables metadata files are optional. |
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202 If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created. |
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203 |
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204 |
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205 Global input files: |
2
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206 ------------------- |
0
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207 |
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208 +-----------------------------+------------+ |
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209 | Parameter : num + label | Format | |
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210 +=============================+============+ |
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211 | 1 : Samples metadata | tabular | |
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212 +-----------------------------+------------+ |
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213 |
4
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214 1. Samples metadata structure |
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215 Samples metadata is in tabular format (.tsv). |
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216 The first column contains the sample names. |
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217 The first row contains the metadata column names. |
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218 Samples names must be in the same order in samples metadata (transposed) and all the blocks. One of the column (the last by default) must contain the samples groups for integration. |
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219 |
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220 ---------- |
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221 Parameters |
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222 ---------- |
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223 |
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224 For each block (min 2 blocks): |
2
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225 ------------------------------ |
0
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226 |
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227 Block name |
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228 Name of the block. If not provided, this will default to the input filename |
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229 |
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230 Number of variables to select for each component |
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231 If set to 0 (default), all variables will be considered in the model |
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232 |
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233 Global parameters: |
2
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234 ------------------ |
0
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235 |
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236 Sample description column number |
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237 |
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238 Number of components to include in the model |
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239 |
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240 Correlation between all blocks |
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241 |
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242 Advanced options: |
2
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243 ----------------- |
0
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244 |
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245 Scheme |
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246 |
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247 Mode |
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248 |
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249 Maximum number of iterations |
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250 |
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251 Scale |
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252 |
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253 Init |
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254 |
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255 Convergence stopping value (tol) |
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256 |
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257 Near zero var |
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258 |
2
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259 |
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260 @HELP_MANUAL@ |
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261 |
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262 ------------ |
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263 Output files |
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264 ------------ |
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265 |
2
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266 mixomics_blocksplsda_output.RData |
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267 | RData output |
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268 | Contains the `mixomics_result` R object containing the result of the block.splsda function |
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269 |
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270 mixomics_blocksplsda_blocks_output |
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271 A collection with the variable metadata output files (mixomics_blocksplsda_block_{block name}_variable_metadata) for each input block |
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272 |
2
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273 ]]></help> |
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274 |
2
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275 <expand macro="citations" /> |
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276 |
4
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277 </tool> |