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annotate sc3-calc-transfs.xml @ 0:ed7d0532545c draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
author ebi-gxa
date Wed, 13 Mar 2019 17:38:56 -0400
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ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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1 <?xml version="1.0" encoding="utf-8"?>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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2 <tool id="sc3_calc_transfs" name="SC3 Calculate Transformations" version="@TOOL_VERSION@+galaxy0">
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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3 <description>of distances using PCA and graph Laplacian</description>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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4 <macros>
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5 <import>sc3-macros.xml</import>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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6 </macros>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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7 <expand macro="requirements" />
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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8 <command detect_errors="exit_code"><![CDATA[
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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9 sc3-sc3-calc-transfs.R -i '${sc3_distances}' -o '${sc3_transformed}'
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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10 ]]></command>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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11
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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12 <inputs>
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13 <param name="sc3_distances" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with distances calculated"/>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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14 </inputs>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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15
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16 <outputs>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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17 <data name="sc3_transformed" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment object with transformed distances"/>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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18 </outputs>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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19
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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20 <tests>
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21 <test>
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22 <param name="sc3_distances" value="sc3_distances.rdata"/>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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23 <output name="sc3_transformed" file="sc3_transformed.rdata"/>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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24 </test>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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25 </tests>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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26
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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27 <help><![CDATA[
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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28 ==============================================
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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29 This function calculate transformed distances.
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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30 ==============================================
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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31
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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32 All items of the sc3 slot of the metadata(object) are transformed using either
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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33 principal component analysis (PCA) or by calculating the eigenvectors of the
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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34 associated graph Laplacian. The columns of the resulting matrices are then
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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35 sorted in descending order by their corresponding eigenvalues. The first d
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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36 columns (where d = max(metadata(object)$sc3$n_dim)) of each transformation are
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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37 then written to the transformations item of the sc3 slot. Additionally, this
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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38 function also removes the previously calculated distances from the sc3 slot, as
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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39 they are not needed for further analysis.
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40
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41 @HELP@
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42
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43 @VERSION_HISTORY@
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44 ]]></help>
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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45 <expand macro="citations" />
ed7d0532545c planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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46 </tool>