<tool id="glytools_lc_extend" name="GAP Permute Linearcode" version="0.3">
    <description> and append or extend fragments on fuzzy linear code </description>
    <requirements>
        <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
    </requirements> 
    <command interpreter="python"><![CDATA[lc_extend.py -i $input -o $output -l $logfile $appendorextend ]]></command>
    <inputs>
        <param format="linearcode" name="input" type="data" label="Linear Code source file"/>
        <param name="appendorextend" type="select" label="Behaviour">
          <option value="" selected="true"> Default append behaviour</option>
          <option value="-e">Create all possible linearcode combinations (not recommended)</option>
        </param>
    </inputs>
    <outputs>
        <data format="linearcode" name="output" label="LC permutations of $input.name"/>
        <data format="txt" name="logfile" label="debugging log file of $input.name"/>
    </outputs>
    <help> <![CDATA[ 
.. class:: infomark

**What this tool does**

This tool provides all permutations of linear code with uncertain leaves i.e. that is it converts fuzzy glycans to unfuzzy glycans.

.. class:: infomark

**Inputs**

This tool requires *LinearCode* format.

----

.. class:: infomark

**Example**

Query sequence::

 (Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN,M)
 (A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)

 Default Output sequence::

 ((M??)X??)(Ma2Ma3(Ma3)(Ma6)Ma6)Mb4GNb4GN
 (A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)

 Extended Output sequence (not recommended)::

 M??Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN
 Ma2Ma3(M??Ma3(Ma6)Ma6)Mb4GNb4GN
 Ma2Ma3(Ma3(M??Ma6)Ma6)Mb4GNb4GN
 (A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)

]]>

</help>

</tool>