Mercurial > repos > ebi-gxa > scpred_train_model

annotate scpred_train_model.xml @ 1:01493c9cdfa7 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
author ebi-gxa
date Fri, 24 Apr 2020 11:27:27 -0400
parents b17acf485397
children 46c2b1454118
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b17acf485397 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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1 <tool id="scpred_train_model" name="Scpred train" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Train classification model</description>
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3 <macros>
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4 <import>scpred_macros.xml</import>
b17acf485397 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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5 </macros>
b17acf485397 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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01493c9cdfa7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
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8 scpred_train_model.R --input-object "${input_object}" --model "${model}" --output-path "${output_obj_path}" --train-probs-plot "${train_probs_plot}"
01493c9cdfa7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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9 #if $train_id
01493c9cdfa7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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10 --train-id '${train_id}'
01493c9cdfa7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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11 #end if
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12 ]]></command>
b17acf485397 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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13 <inputs>
b17acf485397 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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14 <param type="data" name="input_object" label="Input SCE object" format="rdata" help="Input SCE object in .rds format"/>
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01493c9cdfa7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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15 <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
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16 <param type="text" name="model" label="Model type to train" value="svmRadial" help="Model type used for training. Must be one of the models supported by Caret package. Default: svmRadial" />
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17 </inputs>
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18 <outputs>
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19 <data name="output_obj_path" format="rdata" />
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20 <data name="train_probs_plot" format="png" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input_object" value="scPred_feat_space.rds" />
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25 <output name="output_obj_path" file="scPred_trained.rds" compare="sim_size" />
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26 </test>
b17acf485397 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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27 </tests>
b17acf485397 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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28 <help><![CDATA[
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29 @HELP@
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30
b17acf485397 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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31 @VERSION_HISTORY@
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32 ]]></help>
b17acf485397 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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33 <expand macro="citations" />
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34 </tool>