view filter_by_fasta_ids.xml @ 1:8d15aebf55fd draft

planemo upload commit 88309fbfadbafe82f2d8fb7b96468799f2421e30

<tool id="filter_by_fasta_ids" version="1.0" name="Filter by FASTA IDs">
    <description>Extract sequences from a FASTA file based on a list of IDs</description>
    <command>
<![CDATA[
        python $__tool_directory__/filter_by_fasta_ids.py
            $dedup
            '$identifiers'
            '$input'
            '$output'
]]>
    </command>
    <inputs>
        <param format="fasta" name="input" type="data" label="FASTA sequences"/>
        <param format="txt" name="identifiers" type="data" label="List of IDs to extract sequences for"/>
        <param name="dedup" type="boolean" truevalue="--dedup" falsevalue="" checked="true" label="Remove duplicate sequences" />
    </inputs>
    <outputs>
        <data format="fasta" name="output" label="FASTA sequences for ${identifiers.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="fasta" value="input.fasta" />
            <param name="identifiers" ftype="txt" value="ids.txt" />
            <output name="output" file="output_dedup.fasta" />
        </test>
        <test>
            <param name="input" ftype="fasta" value="input.fasta" />
            <param name="identifiers" ftype="txt" value="ids.txt" />
            <param name="dedup" value="False" />
            <output name="output" file="output_not_dedup.fasta" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Extract sequences from a FASTA file based on a list of IDs.
]]>
    </help>
</tool>