comparison crt.xml @ 0:ad026c2db3e9 draft

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<tool id="crispr_recognition_tool" name="CRISPR Recognition Tool" version="1.2.0">
    <description>(CRT)</description>
    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="1" merge_outputs="output,output_region" />
    <requirements>
        <requirement type="package" version="1.2">crisper_recognition_tool</requirement>
        <requirement type="set_environment">CRISPR_RECOGNITION_TOOL_SCRIPT_PATH</requirement>
    </requirements>
    <stdio>
        <exit_code range=":-1" level="fatal" />
        <exit_code range="1:" level="fatal" />
    </stdio>
    <command>
        temp_output=\$(mktemp);
        java -cp \$CRISPR_RECOGNITION_TOOL_JAR_PATH/CRT1.2-CLI.jar crt
            -minNR $minNR
            -minRL $minRL
            -maxRL $maxRL
            -minSL $minSL
            -maxSL $maxSL
            #if str($searchWL) != 'none':
                -searchWL $searchWL
            #end if
            $input
            \$temp_output
            ;

            python \$CRISPR_RECOGNITION_TOOL_SCRIPT_PATH/reformat.py \$temp_output $output_region $output
    </command>
    <inputs>
        <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/>

        <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/>
        <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/>
        <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/>
        <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/>
        <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/>
        <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs">
            <option value="none" selected="true">default</option>
            <option value="6">6</option>
            <option value="7">7</option>
            <option value="8">8</option>
            <option value="9">9</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
        <data format="bed" name="output_region" label="${tool.name} on ${on_string} - BED file" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="sequence.fasta" ftype="fasta" />
            <param name="minNR" value="3" />
            <param name="minRL" value="29" />
            <param name="maxRL" value="38" />
            <param name="minSL" value="19" />
            <param name="maxSL" value="48" />
            <param name="searchWL" value="none" />
            <output name="output" file="crt.tabular" ftype="tabular" />
            <output name="output_region" file="crt.bed" ftype="bed" />
        </test>
    </tests>
    <help>
CRISPR Recognition Tool - a tool for automatic detection of clustered regularly interspaced palindromic repeats

http://www.room220.com/crt/

**Citation**

For the underlying tool, please cite `Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P:
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209`

    </help>
</tool>