comparison find_subsequences.xml @ 1:d882a0a75759 draft default tip

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0:7f39014f9404

<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.1">
    <description>providing regions in BED format</description>
    <requirements>
        <requirement type="package" version="1.65">biopython</requirement>
    </requirements>
    <command interpreter="python">
    <![CDATA[
        find_subsequences.py
            --input $input
            --output $output
            --pattern "$pattern_conditional.pattern"
            #if $input.ext == 'fasta':
                --format 'fasta'
            #else:
                --format 'fastq'
            #end if
    ]]>
    </command>
    <inputs>
        <param format="fasta,fastq" name="input" type="data" label="Nucleotide sequence to be searched"
            help="This can be in FASTA or FASTQ format." />

                <param name="pattern" type="text" value="" label="Search pattern" help="For example GGATCC for BamHI.">
                    <validator type="regex" message="Only letters are allowed.">^[a-zA-Z]+$</validator>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bed" name="output" />
    </outputs>
    <tests>

        <test>
            <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/>
            <param name="pattern" value="atnncg"/>
            <param name="pattern_conditional_select" value="user"/>
            <output name="output" file="find_subsequences_advanced_result1.bed" ftype="bed"/>
        </test>
    </tests>
    <help>
<![CDATA[

1:d882a0a75759

<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.2">
    <description>providing regions in BED format</description>
    <requirements>
        <requirement type="package" version="1.65">biopython</requirement>
    </requirements>
    <command interpreter="python">
    <![CDATA[
        find_subsequences.py
            --input "${input}"
            --output "${output}"
            --pattern "$pattern_conditional.pattern"
            #if $input.ext == 'fasta':
                --format 'fasta'
            #else:
                --format 'fastq'
            #end if
            --strand '$strand'
    ]]>
    </command>
    <inputs>
        <param format="fasta,fastq" name="input" type="data" label="Nucleotide sequence to be searched"
            help="This can be in FASTA or FASTQ format." />

                <param name="pattern" type="text" value="" label="Search pattern" help="For example GGATCC for BamHI.">
                    <validator type="regex" message="Only letters are allowed.">^[a-zA-Z]+$</validator>
                </param>
            </when>
        </conditional>
        <param name="strand" type="select" label="Search pattern on">
            <option value='both'>both strands</option>
            <option value='forward'>forward strand</option>
            <option value='reverse'>reverse strand</option>
        </param>
    </inputs>
    <outputs>
        <data format="bed" name="output" />
    </outputs>
    <tests>

        <test>
            <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/>
            <param name="pattern" value="atnncg"/>
            <param name="pattern_conditional_select" value="user"/>
            <output name="output" file="find_subsequences_advanced_result1.bed" ftype="bed"/>
        </test>
        <test>
            <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/>
            <param name="pattern" value="atnncg"/>
            <param name="strand" value="reverse"/>
            <param name="pattern_conditional_select" value="user"/>
            <output name="output" file="find_subsequences_advanced_result2.bed" ftype="bed"/>
        </test>
        <test>
            <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/>
            <param name="pattern" value="atnncg"/>
            <param name="strand" value="forward"/>
            <param name="pattern_conditional_select" value="user"/>
            <output name="output" file="find_subsequences_advanced_result3.bed" ftype="bed"/>
        </test>
    </tests>
    <help>
<![CDATA[