Mercurial > repos > ebi-gxa > scmap_select_features

annotate scmap_select_features.xml @ 4:d85fba139f9a draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6e7bba7c35bcd8d18c53ca8c51f1699f62e2a836"
author ebi-gxa
date Wed, 29 Apr 2020 09:58:45 -0400
parents 3e22b96ba4fb
children 5972aea41e0e
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d85fba139f9a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6e7bba7c35bcd8d18c53ca8c51f1699f62e2a836"
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1 <tool id="scmap_select_features" name="Scmap select features" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>finds the most informative features (genes/transcripts) for projection.</description>
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3 <macros>
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4 <import>scmap_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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953c7ff4069e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b9472e45f909300389b426955f4f563b8428ed07
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8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-select-features.R --input-object-file "${input_single_cell_experiment}.preprocessed" --n-features '$n_features' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
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9 ]]></command>
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10 <inputs>
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11 <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object" />
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12 <param name="n_features" type="integer" label="Number of features" value="500" help="Number of features to be selected" />
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13 </inputs>
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14 <outputs>
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15 <data name="output_single_cell_experiment" format="rdata" />
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16 <data name="plot" format="png" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input_single_cell_experiment" value="test_sce.rds" ftype="rdata"/>
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21 <output name="output_single_cell_experiment" file="select_features.rds" compare="sim_size"/>
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22 <output name="plot" file="select_features.png" compare="sim_size"/>
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23 </test>
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24 </tests>
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25 <help><![CDATA[
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26 @HELP@
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28 @VERSION_HISTORY@
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29 ]]></help>
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30 <expand macro="citations" />
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31 </tool>