view scmap_scmap_cluster.xml @ 4:6651208d890b draft

"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 10:05:16 -0400
parents 97922339644a
children 40e10f3a1844
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<tool id="scmap_scmap_cluster" name="Scmap cluster projection" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>projects one dataset to another</description>
    <macros>
        <import>scmap_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scmap-scmap-cluster.R --index-object-file '$index_single_cell_experiment' --projection-object-file '$project_single_cell_experiment' --threshold '$threshold' --output-object-file '$output_single_cell_experiment' --output-text-file '$output_txt'
    ]]></command>
    <inputs>
        <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected." />
        <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index'" />
        <param name="threshold" type="float" label="Threshold" value="0.7" help="Threshold on similarity (or probability for SVM and RF)." />
    </inputs>
    <outputs>
        <data name="output_single_cell_experiment" format="rdata" />
        <data name="output_txt" format="csv" />
    </outputs>
    <tests>
        <test>
            <param name="index_single_cell_experiment" value="index_cluster.rds" ftype="rdata"/>
            <param name="project_single_cell_experiment" value="test_sce.rds" ftype="rdata"/>
            <output name="output_single_cell_experiment" file="project_cluster.rds" compare="sim_size"/>
            <output name="output_txt" file="project_cluster.csv" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>