annotate garnett_check_markers.xml @ 1:c00e672eadbc draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

<tool id="garnett_check_markers" name="Garnett - check markers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Check marker file to filter out markers of suboptimal quality</description>
    <macros>
        <import>garnett_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        garnett_check_markers.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --marker-output-path '${marker_output_path}'

        #if $cds_gene_id_type
        --cds-gene-id-type '${cds_gene_id_type}' 
        #end if
        #if $marker_file_gene_id_type
        --marker-file-gene-id-type '${marker_file_gene_id_type}'
        #end if
        #if $plot_output_path
        --plot-output-path '${plot_output_path}' 
        #end if
        #if $propogate_markers
        --propogate-markers '${propogate_markers}'  
        #end if
        #if $propogate_markers
        --classifier-gene-id-type '${classifier_gene_id_type}'
        #end if
    ]]></command>
    <inputs>
        <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" />
        <param type="data" name="marker_file_path" format="txt" label="Marker file path" help="File with marker genes specifying cell types. 
        See https://cole-trapnell-lab.github.io/garnett/docs/#constructing-a-marker-file for specification of the file format" />
        <param type="text" name="database" label="gene database" value="org.Hs.eg.db" help="argument for Bioconductor AnnotationDb-class package used for converting gene IDs" />
        <param type="text" name="cds_gene_id_type" label="CDS gene id type" value="ENSEMBL" help="Format of the gene IDs in your CDS object" />
        <param type="text" name="marker_file_gene_id_type" label="Marker gene id type" value="ENSEMBL" help="Format of the gene IDs in your marker file" />
        <param type="boolean" name="propogate_markers" checked="true" label="propogate markers" help="Should markers from child nodes of a cell type be used
        in finding representatives of the parent type?" />
        <param type="text" name="classifier_gene_id_type"  label="Classifier gene ID type" value="ENSEMBL" help="The type of gene ID that will be used in the classifier. If possible for your organism, this should be 'ENSEMBL', which is the default." />
    </inputs>
    <outputs>
        <data name="marker_output_path" format="txt" />
        <data name="plot_output_path" format="png" />
    </outputs>
    <tests>
        <test>
            <param name="cds_object" value="garnett_cds.rds" />
            <param name="marker_file_path" value="markers_transformed.txt" />
            <output name="marker_output_path" value="marker_check.txt" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
        @HELP@

        @VERSION_HISTORY@
    ]]></help>
     <expand macro="citations" />
</tool>