<tool id="symlink_files" name="Symlink Files" version="0.1.3">
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        #if $__user_email__ not in $__admin_users__:
            exit 1
        #end if

        #if $input:
            mkdir -p '$output_path' &&
            #if '$input.ext':
                #if input.ext == 'bam':
                    ln -fs '$input.metadata.bam_index' '$output_path'/'$input.element_identifier'.'$input.ext'.bai &&
                #end if
               ln -fs \$(readlink '$input') '$output_path'/'$input.element_identifier'.'$input.ext'
            #else:
               ln -fs \$(readlink '$input') '$output_path'/'$input.element_identifier'
            #end if
        #end if
        #if $input_collection:
            mkdir -p '$output_path'/'$input_collection.name' &&
            #for $element in $input_collection:
                #if $element.ext == 'bam':
                    ln -fs '$element.metadata.bam_index' '$output_path'/'$input_collection.name'/'$element.element_identifier'.'$element.ext'.bai &&
                #end if
                    ln -fs \$(readlink '$element') '$output_path'/'$input_collection.name'/'$element.element_identifier'.'$element.ext';
            #end for
        #end if
        #if $input_collection_paired:
            mkdir -p '$output_path'/'$input_collection_paired.name' &&
            #for $element in $input_collection_paired:
                ln -fs \$(readlink '$element.forward') '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-forward.'$element.ext';
                ln -fs \$(readlink '$element.reverse') '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-reverse.'$element.ext';
            #end for
        #end if
        #if $input_collection_list_paired:
            #for $sample in $input_collection_list_paired:
            mkdir -p '$output_path'/'$input_collection_list_paired.name' &&
                #for $element in $sample:
                    ln -fs \$(readlink '$element') '$output_path'/'$input_collection_list_paired.name'/'$sample.name'-$element.element_identifier.'$element.ext';
                #end for
            #end for
        #end if
    ]]></command>
<inputs>
    <param name="input" optional="true" type="data" help="The file you would like to export"/>
    <param name="input_collection" optional="true" type="data_collection" collection_type="list" help="The collection you would like to export"/>
    <param name="input_collection_paired" optional="true" type="data_collection" collection_type="paired" help="The collection you would like to export"/>
    <param name="input_collection_list_paired" optional="true" type="data_collection" collection_type="list:paired" help="The collection you would like to export"/>
    <param name="output_path" type="text" help="Path to export to"/>
    </inputs>
    <outputs>
    </outputs>
    <help><![CDATA[
        Creates symlinks to specified path.
    ]]></help>
</tool>