view elastic_tool_wrappers_macros.xml @ 0:b503fbd571a6 draft default tip

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<?xml version="1.0" encoding="UTF-8"?>
<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="2.3.4.1">bowtie2</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>
  <!--Tool name-->
  <xml name="tool_name">
    <param type="select" name="tool_name" multiple="false" label="Tool name">
        <option value="bowtie2" selected="false">bowtie2</option><option value="bowtie2-build" selected="false">bowtie2-build</option><option value="bowtie2-inspect" selected="false">bowtie2-inspect</option></param>
  </xml>
  <!--OPTION/ARGUMENT PAIRS and INPUT types-->
  <!--input files-->
  <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>
  <!--input path-->
  <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>
  <!--input values: string, float and integer-->
  <xml name="option_argument_string_float_integer">
    <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0" default="0">
      <param type="text" name="flag" label="flag"/>
      <param type="text" name="value" label="value"/>
    </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 &&

        ############ tool_name
        ##-t '$tool_name'
        echo "tool_name|not available|${tool_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>