<?xml version="1.0"?>
<tool name="Search" id="sbtas_se_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'
    
    --search 'rrr'
    --sthreshold ${sthreshold}
    --exact 0
    
    #if $conditional_input_zero.inputtype_zero == '0':
        #set file_paths = ','.join( [ str( $f ) for $f in $conditional_input_zero.txtfiles ] )
        #if $file_paths is not 'None':
            --files '${file_paths}'
            #set file_names = ','.join( [ str( $f.name ) for $f in $conditional_input_zero.txtfiles ] )
                --names '${file_names}'
        #end if
    #elif $conditional_input_zero.inputtype_zero == '1':
        --sequences '${conditional_input_zero.sequences}'
    #end if

    --output '${output}'
]]>
    </command>
    <inputs>
        <conditional name="conditional_input_zero">
            <param name="inputtype_zero" type="select" label="Input mode" help="Select a mode based on how do you want to specify the input">
                <option value="0" selected="true">By file</option>
                <option value="1">By manually inserted text</option>
            </param>
            <when value="0">
                <param format="txt" name="txtfiles" type="data" label="Select sequences" multiple="true" optional="true" help="Select one or more txt files containing a sequence. A single file can contain more sequences, one for each row. Every file will represent a query to the AllSome Sequence Bloom Tree Search Engine that will return a list of accession numbers. It is worth noting that the result could be empty." />
            </when>
            <when value="1">
                <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequence" optional="true" help="Insert a list of sequences (one for each row) in this text field representing a query to the AllSome Sequence Bloom Tree Search Engine. It is worth noting that the result could be empty." />
            </when>
        </conditional>            
        <param name="sthreshold" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Threshold applied to the search algorithm" />
    </inputs>
    <outputs>
        <data name="output" format="json" label="${tool.name} on ${on_string}: AllSome Sequence Bloom Tree Search Result" />
    </outputs>

    <help><![CDATA[
Authors: Fabio Cumbo, Robert S. Harris, Chen Sun
    ]]></help>

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