Mercurial > repos > ebi-gxa > scpred_get_feature_space

annotate scpred_get_feature_space.xml @ 1:4a77d2091aec 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 11:28:26 -0400
parents db7ecc1aaf59
children 2fa2f084ad32
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db7ecc1aaf59 "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_get_feature_space' name='ScPred feature space' version='@TOOL_VERSION@+galaxy0' profile="@PROFILE@">
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2 <description>Get feature space for training matrix</description>
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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3 <macros>
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4 <import>scpred_macros.xml</import>
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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5 </macros>
db7ecc1aaf59 "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' />
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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7 <command detect_errors='exit_code'><![CDATA[
1
4a77d2091aec "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_get_feature_space.R --input-object '${input_object}' --prediction-column '${prediction_column}' --output-path '${output_obj_path}'
4a77d2091aec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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9
4a77d2091aec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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10 #if $explained_var_limit
4a77d2091aec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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11 --explained-var-limit '${explained_var_limit}'
4a77d2091aec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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12 #end if
4a77d2091aec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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13 #if $eigenvalue_plot_path
4a77d2091aec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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14 --eigenvalue-plot-path '${eigenvalue_plot_path}'
4a77d2091aec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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15 #end if
4a77d2091aec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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16 ]]></command>
0
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17 <inputs>
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18 <param type='data' name='input_object' label='Input SCE object' format='rdata' help='Input SCE object in .rds format' />
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19 <param type='text' name='prediction_column' label='Prediction column' help='Name of the metadata column that contains training labels' />
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20 <param type='float' name='explained_var_limit' label='Limit of explained variance' value="0.01" help='Threshold to filter principal components based on variance explained' />
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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21 </inputs>
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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22 <outputs>
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23 <data name='output_obj_path' format='rdata' />
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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24 <data name='eigenvalue_plot_path' format='png' />
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input_object" value="scPred_object.rds" />
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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29 <param name="prediction_column" value="cell_type2" />
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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30 <output name="output_obj_path" file="scPred_feat_space.rds" compare="sim_size" />
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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31 </test>
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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32 </tests>
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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33 <help><![CDATA[
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34 @HELP@
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35
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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36 @VERSION_HISTORY@
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37 ]]></help>
db7ecc1aaf59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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38 <expand macro='citations' />
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39 </tool>