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comparison mixomics_plotvar.xml @ 4:d4e9f7546dfa draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
author ppericard
date Tue, 17 Nov 2020 13:01:44 +0000
parents c8533e9298e5
children 88c1fd2ac110
comparison
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3:df8428358b7f 4:d4e9f7546dfa
1 <tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true"> 1 <tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true">
2 2
3 <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</description> 3 <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
19 $adv.legend 19 $adv.legend
20 --cutoff $adv.cutoff 20 --cutoff $adv.cutoff
21 21
22 --output_pdf $output_pdf 22 --output_pdf $output_pdf
23 23
24 @COMMAND_LOG_EXIT@
25
26 ]]></command> 24 ]]></command>
27 25
28 <inputs> 26 <inputs>
29 <param name="input_rdata" type="data" format="rdata" 27 <param name="input_rdata" type="data" format="rdata"
30 label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)" 28 label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)"
31 help="This is the RData output file from the block.splsda function." /> 29 help="this is the RData output file from the block.splsda function" />
32 <section name="adv" title="Advanced Options" expanded="false"> 30 <section name="adv" title="Advanced Options" expanded="false">
33 <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue="" 31 <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue=""
34 label="Plot legend" /> 32 label="Plot legend" />
35 <param name="cutoff" type="float" value="0" min="0" max="1" 33 <param name="cutoff" type="float" value="0" min="0" max="1"
36 label="Cut-off" 34 label="Cut-off"
37 help="Only selected variables whose correlation with the first or second axis is greater than Cut-off in absolute value will be plotted." /> 35 help="only selected variables whose correlation with the first or second axis is greater than Cut-off in absolute value will be plotted" />
38 </section> 36 </section>
39 </inputs> 37 </inputs>
40 38
41 <outputs> 39 <outputs>
42 <data name="output_pdf" format="pdf" label="plotVar.pdf" /> 40 <data name="output_pdf" format="pdf" label="plotVar.pdf" />
59 57
60 ----------- 58 -----------
61 Description 59 Description
62 ----------- 60 -----------
63 61
64 The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets. 62 This tool allows visualizing the variables of a omics dataset which are correlated with the variables
65 Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA. 63 of the other omic datasets and the response variable in a correlation circle.
66 64
67 ----------------- 65 -----------------
68 Workflow position 66 Workflow position
69 ----------------- 67 -----------------
70 68