view elastic_tool.xml @ 1:58c172729fd3 draft default tip

SRA-Toolkit

<tool id="elastic_sra_toolkit" name="elastic sra-toolkit" version="1.0.0">
    <macros>
        <import>elastic_tool_macros.xml</import>
    </macros>
    <expand macro="tool_description"/>
    <requirements>
        <expand macro="tool_requirements"/>
    </requirements>
    <stdio>
        <regex match="XXX" source="stderr" level="warning"
               description="Check the tool log output file for more details."/>
    </stdio>
    <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|option|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.option) + "|" + 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.option) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|"
            echo '$item' >> $report.files_path/options_and_arguments.txt &&
        #end for


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

        ############ output_set
        ## '$report'
        ## '$report.files_path'
        ## '$tool_output_dir'
        ## '$tool_log'
        #######################
        export REPORT='$report' &&
        export REPORT_FILES_PATH='$report.files_path' &&
        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>
    <inputs>
        <param type="select" name="tool_name" multiple="false" label="Tool name">
            <expand macro="tool_options"/>
        </param>
        <repeat name="option_argument_single_dataset_repeat" title="DATA FROM HISTORY: single data set" min="0"
                default="0">
            <param type="text" name="option" optional="true" label="option"/>
            <param name="value" type="data" optional="false" multiple="false" label="value"/>
        </repeat>
        <repeat name="option_argument_multiple_datasets_repeat" title="DATA FROM HISTORY: multiple data sets"
                min="0" default="0">
            <param type="text" name="option" optional="true" label="option"/>
            <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>
        <repeat name="option_argument_path_relative_to_other_tool_repeat"
                title="PATH: relative to other tool output directory" min="0" default="0">
            <param type="text" name="option" optional="true" label="option"/>
            <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>
        <repeat name="option_argument_path_relative_to_this_tool_repeat"
                title="PATH: relative to this tool output directory" min="0" default="0">
            <param type="text" name="option" optional="true" label="option"/>
            <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>
        <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0"
                default="0">
            <param type="text" name="option" label="option"/>
            <param type="text" name="value" label="value"/>
        </repeat>
    </inputs>
    <outputs>
        <data format="html" name="report" label="${tool.name} report ${on_string}"/>
        <data format="txt" name="tool_output_dir" label="${tool.name} output directory ${on_string}"/>
        <data format="txt" name="tool_log" label="${tool.name} log ${on_string}"/>
    </outputs>
    <expand macro="tool_help" />
    <citations>
        <expand macro="citations"/>
    </citations>
</tool>