view scpred_train_test_split.xml @ 3:7aec34208f30 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit f1471c41f9845cce8b58a51089dcf096c39fe8d6"

<tool id="scpred_traint_test_split" name="Scpred train-test split" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
    <description>CPM normalise and partition into train/test data</description>
    <macros>
        <import>scpred_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scpred_train_test_split.R --input-sce-object "${input_sce_object}"  --training-matrix "${training_mat}" --test-matrix "${test_mat}"  --training-labels "${training_labs}"  --cell-types-column "${cell_types_col}" --test-labels "${test_labs}" 

        #if $norm_counts_slot
        --normalised-counts-slot "${norm_counts_slot}"
        #end if
        #if $training_ratio
        --training-ratio "${training_ratio}" 
        #end if

        ]]></command>
    <inputs>
        <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" />
        <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" />
        <param type="text" name="cell_types_col"  label="Column name for assigned cell types" />
        <param type="float" name="training_ratio" label="Train/test split ratio" value="0.7" help="What proportion of the data set (0 to 1) should be used for training" />
    </inputs>
    <outputs>
        <data name="training_mat" format="rdata" />
        <data name="test_mat" format="rdata" />
        <data name="training_labs" format="txt" />
        <data name="test_labs" format="txt" /> 
    </outputs>
    <tests>
        <test>
            <param name="input_sce_object" value="pollen_cpm.rds" />
            <param name="cell_types_col" value="cell_type2" />
            <output name="training_mat" file="train_matrix.mtx" compare="sim_size"/>
            <output name="test_mat" file="test_matrix.mtx" compare="sim_size"/>
            <output name="training_labs" file="train_metadata.txt" compare="sim_size" />
            <output name="test_labs" file="test_metadata.txt" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>