Mercurial > repos > ppericard > mixomics_blocksplsda
annotate mixomics_plotindiv.xml @ 4:b0ab97ffc2a1 draft
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
author | ppericard |
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date | Mon, 09 Mar 2020 11:53:32 -0400 |
parents | 655d1fbcd3e6 |
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rev | line source |
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b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
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1 <tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="0.3.0" profile="16.04" workflow_compatible="true"> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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2 |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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3 <description>provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA)</description> |
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b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
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4 |
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bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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5 <requirements> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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7 <requirement type="package" version="2.0">r-argparse</requirement> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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8 </requirements> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
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9 |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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10 <stdio> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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11 <!-- <exit_code range="1:" level="fatal" /> --> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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12 </stdio> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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13 |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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14 <command detect_errors="aggressive"> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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15 <![CDATA[ |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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16 Rscript |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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17 ${__tool_directory__}/mixomics_plotindiv_script.R |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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18 --input_rdata $input_rdata |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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19 $adv.legend |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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20 $adv.ellipse |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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21 --output_pdf $output_pdf |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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22 ]]> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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23 </command> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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24 |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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25 <inputs> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
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26 <param name="input_rdata" type="data" format="rdata" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
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27 label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
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28 help="This is the RData output file from the block.splsda function." /> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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29 <section name="adv" title="Advanced Options" expanded="false"> |
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b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
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30 <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue="" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
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31 label="Plot legend" /> |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
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32 <param name="ellipse" type="boolean" checked="true" truevalue="--ellipse" falsevalue="" |
b0ab97ffc2a1
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
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33 label="Plot ellipse plots" /> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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34 </section> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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35 </inputs> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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36 |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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37 <outputs> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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38 <data name="output_pdf" format="pdf" label="plotIndiv.pdf" /> |
bea08702ed51
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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39 </outputs> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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40 |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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41 <tests> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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42 <test> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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43 <param name="input_rdata" value="out_rdata.rdata" /> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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44 <output name="output_pdf" value="out_plotIndiv.pdf" /> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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45 </test> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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46 </tests> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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47 |
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48 <help> |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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49 <![CDATA[ |
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50 .. class:: infomark |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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51 |
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52 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr) |
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53 |
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54 --------------------------------------------------- |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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55 |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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56 .. class:: infomark |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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57 |
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58 **Please cite** |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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59 |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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60 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration. |
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61 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752 |
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62 |
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63 --------------------------------------------------- |
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64 |
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65 ================== |
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66 mixOmics plotIndiv |
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67 ================== |
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68 |
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69 ----------- |
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70 Description |
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71 ----------- |
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72 |
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73 The plotIndiv function is part of the mixOmics package for exploration and integration of Omics datasets. |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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74 Provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA). |
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75 |
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76 ----------- |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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77 Input files |
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78 ----------- |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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79 |
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80 +-------------------------------+------------+ |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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81 | Parameter : num + label | Format | |
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82 +===============================+============+ |
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83 | 1 : Rdata block.splsda output | Rdata | |
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84 +-------------------------------+------------+ |
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85 |
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86 ---------- |
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87 Parameters |
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88 ---------- |
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89 |
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90 Advanced options: |
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91 ================= |
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92 |
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93 Plot legend |
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94 |
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95 Plot ellipse plots |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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96 |
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97 ------------ |
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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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98 Output files |
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99 ------------ |
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100 |
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101 plotIndiv.pdf |
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102 A pdf file with scatter plots for individuals |
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103 |
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104 ]]> |
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105 </help> |
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106 |
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107 <citations> |
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108 <citation type="doi">10.1371/journal.pcbi.1005752</citation> |
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109 </citations> |
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110 |
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111 </tool> |