Mercurial > repos > ebi-gxa > scmap_index_cell

annotate scmap_index_cell.xml @ 2:dd2a84734b87 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
author ebi-gxa
date Fri, 03 Apr 2020 06:36:06 -0400
parents 17b3d7e04b3c
children 5593b0744de9
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dd2a84734b87 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
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1 <tool id="scmap_index_cell" name="scmap index cells" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>creates a cell index for a dataset to enable fast approximate nearest neighbour search</description>
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3 <macros>
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4 <import>scmap_macros.xml</import>
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5 </macros>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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dd2a84734b87 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-index-cell.R --input-object-file "${input_single_cell_experiment}.preprocessed" --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
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9 ]]></command>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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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 as produced by 'scmap select features'" />
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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12 <param name="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" />
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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13 <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" />
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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14 <param name="random_seed" type="integer" label="Random seed" value='1' help="scmap-cell contains k-means step which makes it stochastic, i.e. running it multiple times will provide slightly different results. A fixed random seed ensures reproducibility." />
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15 </inputs>
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16 <outputs>
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17 <data name="output_single_cell_experiment" format="rdata" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="n_chunks" value="50" />
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22 <param name="n_clusters" value="9" />
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23 <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
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dd2a84734b87 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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24 <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/>
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25 </test>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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26 </tests>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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27 <help><![CDATA[
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28 @HELP@
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30 @VERSION_HISTORY@
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31 ]]></help>
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32 <expand macro="citations" />
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33 </tool>