annotate rdeval_report.xml @ 5:7cfeba6facd1 draft

planemo upload for repository https://github.com/vgl-hub/rdeval commit d55c4b3d6b91d0418950ed6b7806ef779a916099

<tool id="rdeval_report" name="rdeval report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Read summary and figures.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
    mkdir render &&
    cd render &&
    export RDEVAL_SHARE_DIR="\$(dirname \$(dirname \$(type -P rdeval)))/share/rdeval" &&
    ln -s "\$RDEVAL_SHARE_DIR/figures.Rmd" &&
    ln -s "\$RDEVAL_SHARE_DIR/rdeval_interface.R" &&
    #set $input_file_list = []
    #for $idx, $input_file in enumerate($input_files)
        ln -s '$input_file' '${idx}.rd' &&
        #silent $input_file_list.append(f"'{idx}.rd'")
    #end for
    #set $r_vector = "c(" + ",".join(input_file_list) + ")"
    #set $interactive_value = "FALSE"
    #if $output_format.format_selector == "html" and $output_format.interactive
        #set $interactive_value = "TRUE"
    #end if
    R -e "rmarkdown::render('figures.Rmd', output_file='$outfile', output_format='${output_format.format_selector}_document', params=list(input_files=$r_vector, interactive='$interactive_value'))"
	]]></command>
    <inputs>
        <param name="input_files" type="data" format="data" multiple="true" label="Input dataset" help="RD files"/>
        <conditional name="output_format">
            <param name="format_selector" type="select" label="output format" help="output format">
                <option value="html" selected="true">html</option>
                <option value="pdf">pdf</option>
            </param>
            <when value="html">
                <param name="interactive" type="boolean" value="true" label="interactive" help="interactive"/>
            </when>
            <when value="pdf"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="outfile" format="html" label="Rdeval report">
            <change_format>
                <when input="output_format" value="pdf" format="pdf"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_files" value="input1.rd"/>
            <conditional name="output_format">
                <param name="format_selector" value="html"/>
            </conditional>

            <output name="outfile" ftype="html">
                <assert_contents>
                    <has_size size="833000" delta="8330"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This tool creates a report containing a read summary and figures from input RD files.
    ]]></help>
    <expand macro="citations"/>
</tool>