annotate scpred_eigen_decomp.xml @ 2:70e5a19d9d7e draft

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

<tool id="scpred_eigen_decompose" name="Scpred eigen-decompose" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Perform matrix eigen-decomposition; initialize object of scPred class</description>
    <macros>
         <import>scpred_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scpred_eigen_decomp.R --training-matrix "${training_matrix}" --training-labels "${training_labels}"  --output-path "${output_object_path}"

        #if $log_transform
        --log-transform "${log_transform}" 
        #end if
        #if $principal_components
        --principal-comps "${principal_components}"
        #end if
         ]]></command>
    <inputs>
        <param type="data" name="training_matrix" label="Training matrix" format="rdata" help="Training matrix obtained from train/test split step" />
        <param type="boolean" name="log_transform" label="log-transform" checked="True" help="Should log-transform be performed on training data?" />
        <param type="data" name="training_labels" label="training labels file" format="txt" help="Path to training labels in text format" />
        <param type="integer" name="principal_components" label="Number of pincipal components" value="10" help="Number of principal components" />
    </inputs>
    <outputs>
        <data name="output_object_path" format="rdata" />
    </outputs>
    <tests>
        <test>
            <param name="training_matrix" value="train_matrix.mtx" />
            <param name="training_labels" value="train_metadata.txt" />
            <output name="output_object_path" file="scPred_object.rds" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>