view fasta_filter_by_length.xml @ 4:8cacfcf96a52 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"

<tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.2" profile="16.04">
    <description></description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command>
python '$__tool_directory__/fasta_filter_by_length.py' '$input' $min_length $max_length '$output'
    </command>
    <inputs>
        <param name="input" type="data" format="fasta" label="Fasta file"/>
        <param name="min_length" type="integer" value="0" label="Minimal length" />
        <param name="max_length" type="integer" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/> 
    </inputs>
    <outputs>
        <data name="output" format="fasta"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="454.fasta" />
            <param name="min_length" value="10" />
            <param name="max_length" value="0" />
            <output name="output" file="fasta_tool_filter_length_1.out" />
        </test>
        <test>
            <param name="input" value="4.fasta" />
            <param name="min_length" value="0" />
            <param name="max_length" value="60" />
            <output name="output" file="fasta_tool_filter_length_2.out" />
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**TIP**. To return sequences longer than a certain length, set *Minimal length* to desired value and leave *Maximum length* set to '0'.

-----

**What it does**

Outputs sequences greater than or equal to *Minimal length* and less than or equal to *Maximum length*. 
 
-----

**Example**

Suppose you have the following FASTA formatted sequences::

    >seq1
    TCATTTAATGAC
    >seq2
    ATGGC
    >seq3
    TCACATGATGCCG
    >seq4
    ATGGAAGC

Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp::

    >seq1
    TCATTTAATGAC
    >seq3
    TCACATGATGCCG


    ]]></help>
</tool>