annotate scmap_get_std_output.xml @ 3:3370352d1f85 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6e7bba7c35bcd8d18c53ca8c51f1699f62e2a836"

<tool id="scmap_get_std_output" name="Scmap get standard output" version="@TOOL_VERSION@+galaxy2"  profile="@PROFILE@">
    <description>Create final output in standard format to allow for downstream analysis of predicted labels by tools of the EBI gene expression group's cell-types-analysis package</description>
    <macros>
         <import>scmap_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}" --index '${index}' --tool '${tool}' --sim-col-name "${sim_col_name}"
    ]]></command>
    <inputs>
        <param type="data" name="input_predictions_file" label="Scmap predictions file in text format" format="txt" help="Path to the predictions file in text format" />
        <param type="boolean" name="include_scores" checked="false"  label="Should prediction scores be included?" help="Boolean indicating whether similarity scores should be included in the final output" />
        <param type="data" name="index" label="Scmap index object" format="rdata" help="Scmap index object in rdata format" />
        <param type="select" name="tool" label="Tool used (cell/cluster)"  help="What tool was used - scmap-cell or scmap-cluster?">
            <option value="scmap-cell">Scmap-cell</option>
            <option value="scmap-cluster">Scmap-cluster</option>
        </param>
        <param type="text" name="sim_col_name" value="scmap_cluster_siml" label="Column name of similarity scores" help="Name of column that contains distances between clusters/cells" />
    </inputs>
    <outputs>
        <data name="output_predictions_file" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input_predictions_file" value="project_cluster.csv" />
            <param name="include_scores" value="TRUE" />
            <output name="output_predictions_file" value="scmap_output_tbl.txt" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    Generate output tables in tab-separated format compatible with input specified in cell-types-analysis package: https://github.com/ebi-gene-expression-group/cell-types-analysis. 
    See the example snippet below: 
    ________________________________________
    |  cell_id   | predicted_label | score |
    | ERR2632411 | memory B cell   |  0.8  |
    ...
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>