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<?xml version="1.0"?>
<tool name="Search" id="srase_search" version="1.0.0">
    <description>your sequences in the big SRA data lake</description>
    <requirements>
        <requirement type="package" version="2.7.10">python</requirement>
        <requirement type="package" version="2.18.4">requests</requirement>
        <requirement type="package" version="0.9.7">requests-futures</requirement>
    </requirements>
    <command detect_errors="exit_code">
<![CDATA[
    python '$__tool_directory__/search.py'
    
    #if $search_condition.sequences:
        --sequences '${search_condition.sequences}'
    #end if
    --search ${search_condition.search}
    
    #if $search_condition.search is 0:
        #set file_paths = ','.join( [ str( $f ) for $f in $search_condition.txtfiles ] )
        #if $file_paths is not 'None':
            --files '${file_paths}'
            #set file_names = ','.join( [ str( $f.name ) for $f in $search_condition.txtfiles ] )
                --names '${file_names}'
        #end if
    #elif $search_condition.search is 1:
        #set file_paths = ','.join( [ str( $f ) for $f in $search_condition.fastafiles ] )
        #if $file_paths is not 'None':
            --files '${file_paths}'
            #set file_names = ','.join( [ str( $f.name ) for $f in $search_condition.fastafiles ] )
                --names '${file_names}'
        #end if
        --exact ${search_condition.exact}
    #end if

    --sthreshold '${sthreshold}'
    --output '${output}'
]]>
    </command>
    <inputs>
        <conditional name="search_condition">
            <param name="search" type="select" label="Search mode" help="Select a search mode between normal (slower but returns an optimal solution) and fast (faster but it is heuristic)">
                <option value="0" selected="true">Normal</option>
                <option value="1">Fast</option>
            </param>
            <when value="0">
                <param format="txt" name="txtfiles" type="data" label="Select sequences" multiple="true" optional="true" help="Select one or more txt files containing a sequence. A single file can contain more sequences, one for each row. Every file will represent a query to the Sequence Read Archive Search Engine that will return a list of accession numbers in which your sequences occur on." />
                <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequence" optional="true" help="Optionally you can put a list of sequences (one for each row) in this text field." />
            </when>
            <when value="1">
                <param format="fasta" name="fastafiles" type="data" label="Select fasta files" multiple="true" optional="false" help="Select one or more fasta files containing sequences. These files represent queries to the Sequence Read Archive Search Engine that will return a list of accession numbers in which your sequences occur on." />
                <param name="exact" type="boolean" truevalue="1" falsevalue="0" checked="False" label="Use exact algorithm" help="" />
            </when>
        </conditional>
        <param name="sthreshold" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Threshold applied to the search algorithm" />
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} on ${on_string}: SRA-SE Search Result" />
    </outputs>

    <help><![CDATA[
Authors: Fabio Cumbo, Robert S. Harris, Chen Sun, Paul Medvedev, and Anton Nekrutenko

Help section
    ]]></help>

    <citations>
        <citation type="doi">10.1101/090464</citation>
    </citations>
</tool>