Mercurial > repos > ebi-gxa > garnett_classify_cells

annotate garnett_classify_cells.xml @ 0:67e6c4455bb8 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
author ebi-gxa
date Wed, 08 Apr 2020 06:22:12 -0400
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children ad647e1d14dc
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67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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1 <tool id="garnett_classify_cells" name="Garnett - classify cells" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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2 <description>Classify cells into cell types</description>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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3 <macros>
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4 <import>garnett_macros.xml</import>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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5 </macros>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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6 <expand macro="requirements" />
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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7 <command detect_errors="exit_code"><![CDATA[
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8 garnett_classify_cells.R --cds-object '${cds_object}' --classifier-object '${classifier_object}' --database '${database}' --cds-gene-id-type '${cds_gene_id_type}' --cluster-extend '${cluster_extend}' --rank-prob-ratio '${rank_prob_ratio}' --cds-output-obj '${cds_output_obj}'
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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9 ]]></command>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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10 <inputs>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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11 <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" />
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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12 <param type="data" name="classifier_object" label="classifier object" format="rdata" help="Path to the object of class garnett_classifier, which is either trained via garnett_train_classifier.R or obtained elsewhere" />
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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13 <param type="text" name="database" label="gene database" value="org.Hs.eg.db" help="argument for Bioconductor AnnotationDb-class package used for converting gene IDs" />
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14 <param type="text" name="cds_gene_id_type" label="CDS gene id type" value="ENSEMBL" help="Format of the gene IDs in your CDS object" />
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15 <param type="boolean" name="cluster_extend" checked="true" label="cluster-extended classification" help="Boolean, tells Garnett whether to create a second set of assignments that expands classifications to cells in the same cluster" />
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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16 <param type="float" name="rank_prob_ratio" value="1.5" label="label probability ratio" help="Numeric value greater than 1. This is the minimum odds ratio between the probability of the most likely cell type to the second most likely cell type to allow assignment. Default is 1.5. Higher values are more conservative." />
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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17 </inputs>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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18 <outputs>
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19 <data name="cds_output_obj" format="rdata" />
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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20 </outputs>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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21 <tests>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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22 <test>
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23 <param name="cds_object" value="garnett_cds.rds" />
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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24 <param name="classifier_object" value="trained_classifier.rds" />
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25 <output name="cds_output_obj" value="cds_pred_labs.rds" compare="sim_size" />
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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26 </test>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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27 </tests>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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28 <help><![CDATA[
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29 @HELP@
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31 @VERSION_HISTORY@
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32 ]]></help>
67e6c4455bb8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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33 <expand macro="citations" />
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34 </tool>
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