Mercurial > repos > ebi-gxa > scpred_preprocess_data

annotate scpred_preprocess_data.xml @ 2:cb4ebb47c3b9 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 2f718294665c9d01702ad765904972f463154cd6"
author ebi-gxa
date Fri, 01 May 2020 13:44:56 +0000
parents 39b208cca9f1
children 118f6e04371c
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cb4ebb47c3b9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 2f718294665c9d01702ad765904972f463154cd6"
ebi-gxa
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1 <tool id="scpred_preprocess_data" name="Scpred pre-process" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
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2 <description>Pre-process input dataset (no train/test split)</description>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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3 <macros>
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4 <import>scpred_macros.xml</import>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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5 </macros>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 scpred_preprocess_data.R --input-sce-object "${input_sce_object}" --output-matrix-object "${output_mat_object}"
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
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39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
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10 #if $norm_counts_slot
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
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11 --normalised-counts-slot "${norm_counts_slot}"
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
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12 #end if
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
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13 #if $output_labels
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
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14 --output-labels "${output_labels}"
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
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15 #end if
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39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
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17 ]]></command>
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18 <inputs>
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19 <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" />
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cb4ebb47c3b9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 2f718294665c9d01702ad765904972f463154cd6"
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20 <param type="text" name="norm_counts_slot" optional="true" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" />
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21 </inputs>
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22 <outputs>
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23 <data name="output_mat_object" format="rdata" />
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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24 <data name="output_labels" format="txt" />
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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25 </outputs>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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26 <help><![CDATA[
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27 @HELP@
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29 @VERSION_HISTORY@
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30 ]]></help>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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31 <expand macro="citations" />
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32 </tool>