annotate scmap_get_std_output.xml @ 8:601a933714f1 draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8350493268ce3ced12b1133b9b0f734a288deb75

<tool id="scmap_get_std_output" name="Scmap get standard output" version="@TOOL_VERSION@+galaxy0"  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 "${include_scores}"
        --tool '${tool}'
        --sim-col-name "${sim_col_name}"
        #if $index
          --index "${index}"
        #end if   
    ]]></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" optional="true" 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="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input_predictions_file" value="closest_cells_clusters.tsv" />
            <param name="include_scores" value="TRUE" />
            <output name="output_predictions_file">
                <assert_contents>
                    <has_n_lines n="92"/>
                    <has_text text="predicted_label"/>
                    <has_text text="Zygote..3.RPKM."/>
                </assert_contents>
            </output>
        </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>