<tool id="md_slicer" name="Slice MD trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>using the MDTraj package</description>
    <macros>
        <token name="@TOOL_VERSION@">1.9.7</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">mdtraj</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$traj' traj.${traj.ext} && 
        mdconvert traj.${traj.ext} -o output.${traj.ext} -i $start:$end:$stride && 
        mv output.${traj.ext} '$output'
    ]]></command>
    <inputs>
        <param argument="traj" type="data" format='xtc,dcd' label="Input trajectory file for slicing"/>
        <param argument="start" type="integer" value="0" label="Start frame for slicing"/>
        <param argument="end" type="integer" value="10000" label="End frame for slicing"/>
        <param argument="stride" type="integer" value="1" label="Stride" help="i.e. load every nth frame from the input file"/>
    </inputs>
    <outputs>
        <data name="output" format_source="traj"/>
    </outputs>
    <tests>
        <test>
            <param name="traj" value="traj.xtc" />
            <param name="start" value="0" />
            <param name="end" value="8" />
            <param name="stride" value="2" />
            <output name="output" file="traj_slice.xtc" />
        </test>
        <test>
            <param name="traj" value="traj.dcd" />
            <param name="start" value="1" />
            <param name="end" value="6" />
            <param name="stride" value="1" />
            <output name="output" file="traj_slice.dcd" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**
        
This tool extracts a segment from a molecular dynamcics trajectory (i.e. performs a slice). 

_____


.. class:: infomark

**Input**
 
       - Trajectory file (xtc, dcd)
     
In addition, a start frame and end frame have to be specified for the output trajectory, 
as well as a value for the 'stride' (to save only every nth frame in the output file).
_____

        
.. class:: infomark

**Output**

       - Trajectory file (xtc, dcd) extracted from the input file.
    ]]></help>
    <citations>
        <citation type="doi">10.1016/j.bpj.2015.08.015</citation>
    </citations>
</tool>