Mercurial > repos > ebi-gxa > scpred_traint_test_split
annotate scpred_train_test_split.xml @ 0:8ec19f24fcf3 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
author | ebi-gxa |
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date | Wed, 08 Apr 2020 06:37:16 -0400 |
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children | a6d66c9953ed |
rev | line source |
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8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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1 <tool id="scpred_traint_test_split" name="Scpred train-test split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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2 <description>CPM normalise and partition into train/test data</description> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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3 <macros> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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4 <import>scpred_macros.xml</import> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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5 </macros> |
8ec19f24fcf3
"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" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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7 <command detect_errors="exit_code"><![CDATA[ |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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8 scpred_train_test_split.R --input-sce-object "${input_sce_object}" --normalised-counts-slot "${norm_counts_slot}" --training-matrix "${training_mat}" --test-matrix "${test_mat}" --cell-types-column "${cell_types_col}" --training-labels "${training_labs}" --test-labels "${test_labs}" --training-ratio "${training_ratio}" ]]></command> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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9 <inputs> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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10 <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" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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11 <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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12 <param type="text" name="cell_types_col" label="Column name for assigned cell types" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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13 <param type="float" name="training_ratio" label="Train/test split ratio" value="0.7" help="What proportion of the data set (0 to 1) should be used for training" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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14 </inputs> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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15 <outputs> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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16 <data name="training_mat" format="rdata" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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17 <data name="test_mat" format="rdata" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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18 <data name="training_labs" format="txt" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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19 <data name="test_labs" format="txt" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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20 </outputs> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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21 <tests> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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22 <test> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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23 <param name="input_sce_object" value="pollen_cpm.rds" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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24 <param name="cell_types_col" value="cell_type2" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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25 <output name="training_mat" file="train_matrix.mtx" compare="sim_size"/> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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26 <output name="test_mat" file="test_matrix.mtx" compare="sim_size"/> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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27 <output name="training_labs" file="train_metadata.txt" compare="sim_size" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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28 <output name="test_labs" file="test_metadata.txt" compare="sim_size" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
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29 </test> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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30 </tests> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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31 <help><![CDATA[ |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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32 @HELP@ |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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33 |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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34 @VERSION_HISTORY@ |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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35 ]]></help> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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36 <expand macro="citations" /> |
8ec19f24fcf3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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37 </tool> |