view elastic_r_package_wrappers_macros.xml @ 6:3de03ccbf8fb draft

planemo upload

<macros>

    <xml name="rmarkdown_requirements">
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.6">r-rmarkdown</requirement>
        <requirement type="package" version="1.2.1">r-tidyverse</requirement>
    </xml>

    <xml name="stdio">
        <stdio>
            <regex match="XXX" source="stderr" level="warning"
                   description="Check the tool log output file for more details."/>
        </stdio>
    </xml>

    <xml name="function_components">
        <repeat name="function_component_repeat" title="call a function" min="1" default="1">
            <expand macro="function_name" />
            <expand macro="function_arguments" />
        </repeat>
    </xml>

    <!--Tool name-->
    <xml name="function_name">
        <param type="select" name="function_name" multiple="false" label="==== Call function ====">
            <option value="ggplot" selected="false">ggplot</option>
            <option value="aes" selected="false">ggplot</option>
            <option value="read.table" selected="false">read.table</option>
            <option value="write.csv" selected="false">write.csv</option>
        </param>
    </xml>

    <!--input values: string, float and integer-->
    <xml name="function_arguments">
        <repeat name="regular_argument_value" title="|        INPUT VALUE: from user input" min="0" default="0">
            <param type="text" name="argument" label="argument"  />
            <param type="text" name="argument_value"  label="argument value"  />
            <param type="select" name="argument_type"  label="argument type">
                <option value="string" selected="true">string</option>
                <option value="numeric" selected="true">numeric</option>
                <option value="boolean" selected="true">boolean</option>
            </param>
        </repeat>
        <repeat name="rdata_argument_value" title="|        INPUT VALUE: from RData" min="0" default="0">
            <param type="text" name="argument" label="argument"  />
            <param type="data" format="rdata" name="argument_value" optional="false" label="RData output"  />
        </repeat>
        <repeat name="function_argument_value" title="|        INPUT VALUE: from function return" min="0" default="0">
            <param type="text" name="argument" optional="false" label="argument"  />
            <expand macro="function_name" />
            <expand macro="nested_function_arguments" />
        </repeat>
        <param type="select" name="connect_to_next_function" label="connect to next function">
            <option value="%>%" selected="false">pipe (%>%)</option>
            <option value="+" selected="false">plus (+)</option>
        </param>
    </xml>

    <xml name="nested_function_arguments">
        <repeat name="regular_argument_value" title="|        INPUT VALUE: string/numeric/boolean" min="0" default="0">
            <param type="text" name="argument" label="argument"  />
            <param type="text" name="argument_value"  label="argument value"  />
            <param type="select" name="argument_type"  label="argument type">
                <option value="string" selected="true">string</option>
                <option value="numeric" selected="true">numeric</option>
                <option value="boolean" selected="true">boolean</option>
            </param>
        </repeat>
        <repeat name="rdata_argument_value" title="|        INPUT VALUE: from RData" min="0" default="0">
            <param type="text" name="argument" label="argument"  />
            <param type="text" name="argument_value"  label="RData output"  />
        </repeat>
    </xml>

    <!--&lt;!&ndash;OPTION/ARGUMENT PAIRS and INPUT types&ndash;&gt;-->
    <!--&lt;!&ndash;input files&ndash;&gt;-->
    <!--<xml name="option_argument_single_dataset">-->
        <!--<repeat name="option_argument_single_dataset_repeat" title="INPUT DATA FROM HISTORY: single data set" min="0" default="0">-->
            <!--<param type="text" name="flag" optional="true" label="flag" />-->
            <!--<param name="value" type="data" optional="false" multiple="false" label="value"/>-->
        <!--</repeat>-->
    <!--</xml>-->

    <!--<xml name="option_argument_multiple_datasets">-->
        <!--<repeat name="option_argument_multiple_datasets_repeat" title="INPUT DATA FROM HISTORY: multiple data sets" min="0" default="0">-->
            <!--<param type="text" name="flag" optional="true" label="flag" />-->
            <!--<param name="value" type="data" optional="false" multiple="true" label="value"/>-->
            <!--<param type="select" name="delimiter" multiple="false" label="file delimiter">-->
                <!--<option value=" " selected="false">space</option>-->
                <!--<option value="," selected="false">comma</option>-->
            <!--</param>-->
        <!--</repeat>-->
    <!--</xml>-->

    <!--&lt;!&ndash;input path&ndash;&gt;-->
    <!--<xml name="option_argument_path_relative_to_a_tool">-->
        <!--<repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="0" default="0">-->
            <!--<param type="text" name="flag" optional="true" label="flag"  />-->
            <!--<param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>-->
            <!--<param type="text" name="value" optional="true" label="value"  />-->
        <!--</repeat>-->
    <!--</xml>-->
    <!--<xml name="option_argument_path_relative_to_this_tool">-->
        <!--<repeat name="option_argument_path_relative_to_this_tool_repeat" title="OUTPUT PATH: relative to this tool output directory" min="0" default="0">-->
            <!--<param type="text" name="flag" optional="true" label="flag"  />-->
            <!--<param type="text" name="value" optional="false" label="value"  />-->
            <!--<param type="select" name="path_type" multiple="false" label="path type">-->
                <!--<option value="file_path" selected="false">file path</option>-->
                <!--<option value="dir_path" selected="false">directory path</option>-->
            <!--</param>-->
        <!--</repeat>-->
    <!--</xml>-->



    <!--output set-->
    <xml name="output_set">
        <data format="html" name="report" label="${tool.name} report"/>
        <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
        <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/>
        <data format="txt" name="tool_log" label="${tool.name} log" />
    </xml>


    <!--shell command fragment-->
    <xml name="shell_command">
        <command><![CDATA[

        ############ first, create a directory to store all files
        mkdir -p $report.files_path &&


        ############ save the tool installation directory to an environment variable
        export TOOL_INSTALL_DIR='${__tool_directory__}' &&


        #########################
        ##
        ## save user input option/argument pairs into a file
        ##
        #########################

        ## first line will be the header
        echo 'type|flag|value|path_type' > $report.files_path/options_and_arguments.txt &&

        ############ function_name
        ##-t '$function_name'
        echo "function_name|not available|${function_name}|not available" >> $report.files_path/options_and_arguments.txt &&

        ####################################################
        ## loop through repeats to get option/argument pairs
        ####################################################

        ############ option_argument_single_dataset
        #for i in $option_argument_single_dataset_repeat:
            #set $item = 'single_dataset|' + str($i.flag) + "|" + str($i.value) + "|"
            echo '$item' >> $report.files_path/options_and_arguments.txt &&
        #end for

        ############ option_argument_multiple_datasets
        #for i in $option_argument_multiple_datasets_repeat:
            #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|"
            echo '$item' >> $report.files_path/options_and_arguments.txt &&
        #end for


        ############ option_argument_path_relative_to_a_tool
        #for i in $option_argument_path_relative_to_a_tool_repeat:
             #set $item = 'path_relative_to_a_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir)
             echo '$item' >> $report.files_path/options_and_arguments.txt &&
        #end for

        ############ option_argument_path_relative_to_this_tool
        #for i in $option_argument_path_relative_to_this_tool_repeat:
             #set $item = 'path_relative_to_this_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.path_type)
             echo '$item' >> $report.files_path/options_and_arguments.txt &&
        #end for

        ############ option_argument_string_float_integer
        #for i in $option_argument_string_float_integer_repeat:
             #set $item = 'value|' + str($i.flag) + "|" + str($i.value) + "|"
             echo '$item' >> $report.files_path/options_and_arguments.txt &&
        #end for

        ############ output_set
        ## '$report'
        ## '$report.files_path'
        ## '$tool_help_doc'
        ## '$tool_output_dir'
        ## '$tool_log'
        #######################
        export REPORT='$report' &&
        export REPORT_FILES_PATH='$report.files_path' &&
        export TOOL_HELP_DOC='$tool_help_doc' &&
        export TOOL_OUTPUT_DIR='$tool_output_dir' &&
        export TOOL_LOG='$tool_log' &&


        ############ run render R script to render R markdowns
        Rscript '${__tool_directory__}/elastic_tool_render.R'

        ]]></command>
    </xml>

    <!--tool citations-->
    <xml name="citations">
        <citation type="bibtex"><![CDATA[
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},
            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
            journal={R package version 0.9},
            volume={6},
            year={2016}
            }
        ]]></citation>
        <citation type="bibtex"><![CDATA[
            @book{xie2015elastic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        ]]></citation>
    </xml>
</macros>