annotate trj.xml @ 1:e9cc595562b8 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"

<tool id="gmx_trj" name="Modify/convert GROMACS trajectories" version="@VERSION@">
    <description>using trjconv and trjcat</description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <command detect_errors="exit_code"><![CDATA[

    #if $trj.trj_op == 'trjcat':
        mkdir trajs &&
        #for $value, $file in enumerate($trj_input):
            ln -s '$file' trajs/traj_${value}.${file.ext} &&
        #end for

        gmx trjcat
            -f trajs/traj* ## here we assume that they all have the same ext, probably reasonable
            $trj.cat
            -e '$time.e'

    #elif $trj.trj_op == 'trjconv':
        ln -s '$ndx_input' ./index.ndx &&
        ln -s '$str_input' ./str.${str_input.ext} &&
        ln -s '$trj_input' ./traj.${trj_input.ext} &&
        #if $trj.center:
            echo '$trj.index_center $trj.index_output' | gmx trjconv
        #else
            echo '$trj.index_output' | gmx trjconv
        #end if
            -f ./traj.${trj_input.ext}
            -s ./str.${str_input.ext}
            -n ./index.ndx
            $trj.center
            -pbc $trj.pbc
            -ur $trj.ur
            -boxcenter $trj.boxcenter
            #if $time.e != -1:
                -e '$time.e'
            #end if

    #end if

    -b '$time.b'
    -dt '$time.dt'
    -o ./output.${output_format} &&
    &>> verbose.txt &&
    mv ./output.${output_format} '$output'

    ]]></command>

    <inputs>
        <conditional name="trj">
            <param name="trj_op" type="select" label="Modify a trajectory or concatenate multiple trajectories?">
                <option value="trjconv">Modify (trjconv)</option>
                <option value="trjcat">Concatenate (trjcat)</option>
            </param>
            <when value="trjconv">
                <param name="trj_input" type="data" format='xtc,trr' label="Input trajectory" help="In XTC or TRR format."/>
                <param name="str_input" type="data" format='pdb,gro,tpr' label="Input structure" help="In PDB, GRO or TPR format."/>
                <param name="ndx_input" type="data" format='ndx' label="Index (NDX) file" help="In NDX format."/>
                <param name="index_output" type="text" label="Index of group to save in the output" help="Index of group to save in the output - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).">
                    <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
                </param>
                <param name="center" type="boolean" label="Center system in box" truevalue="-center" falsevalue=""/>
                <param name="index_center" type="text" label="Index of group for centering" optional="true" help="Index of group for centering - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0). Leave blank if centering is not required.">
                    <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
                </param>
                <param name="pbc" type="select" label="PBC treatment" >
                    <option value="none">none</option>
                    <option value="mol">mol</option>
                    <option value="res">res</option>
                    <option value="atom">atom</option>
                    <option value="nojump">nojump</option>
                    <option value="cluster">cluster</option>
                    <option value="whole">whole</option>
                </param>
                <param name="ur" type="select" label="Unit cell representation" >
                    <option value="rect">rect</option>
                    <option value="tric">tric</option>
                    <option value="compact">compact</option>
                </param>
                <param name="boxcenter" type="select" label="Center for PBC and centering treatment" >
                    <option value="rect">rect</option>
                    <option value="tric" selected="true">tric</option>
                    <option value="zero">zero</option>
                </param>
            </when>
            <when value="trjcat">
                <param name="trj_input" type="data" format='xtc,trr' label="Input trajectories" help="In XTC or TRR format, but please do not mix the two. Please note this tool does not currently take order into account when concatenating." multiple="true"/>
                <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/>
            </when>
        </conditional>
        <param name="output_format" type="select" label="Output format" >
            <option value="xtc">XTC</option>
            <option value="trr">TRR</option>
            <option value="pdb">PDB</option>
            <option value="gro">GRO</option>
        </param>
        <section title="Time" name='time' expanded="true">
            <param name="b" type="integer" label="Start time" help="Time (ps) of first frame to read from trajectory" value="0" min="0"/>
            <param name="e" type="integer" label="End time" help="Time (ps) of last frame to read from trajectory" value="-1"  min="-1"/> <!-- stupidly this has different default values for trjconv and trjcat -->
            <param name="dt" type="integer" label="Write frames at this time interval (ps)" help="Only write frame when t is exactly divisible by this value. Leave as 0 to record all frames." value="0"  min="0"/>
        </section>
        <expand macro="log" />
    </inputs>
    <outputs>
        <data name="output" format="xtc">
            <change_format>
                <when input="output_format" value="trr" format="trr"/>
                <when input="output_format" value="xtc" format="xtc"/>
                <when input="output_format" value="gro" format="gro"/>
                <when input="output_format" value="pdb" format="pdb"/>
            </change_format>
        </data>
    </outputs> 
    <tests>
        <test>
            <!-- gmx trjcat -f npt.xtc nvt.xtc -cat -o test.xtc -->
            <param name="trj_op" value="trjcat" />
            <param name="trj_input" value="npt.xtc,nvt.xtc" />
            <param name="b" value="0" />
            <param name="e" value="-1" />
            <param name="dt" value="0" />
            <param name="cat" value="true" />
            <output name="output" file="trjcat.xtc" ftype="xtc"/>
        </test>
        <test>
            <!-- echo '1 1' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -o npt_c.xtc -->
            <param name="trj_op" value="trjconv" />
            <param name="trj_input" value="npt.xtc" />
            <param name="str_input" value="npt.tpr" ftype="tpr"/>
            <param name="ndx_input" value="index.ndx" />
            <param name="b" value="0" />
            <param name="e" value="-1" />
            <param name="dt" value="0" />
            <param name="index_output" value="1" />
            <param name="index_center" value="1" />
            <param name="center" value="true" />
            <param name="pbc" value="mol" />
            <param name="ur" value="compact" />
            <param name="ur" value="tric" />
            <output name="output" file="trjconv.xtc" ftype="xtc"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool allows manipulation of GROMACS trajectories, drawing on the trjcat and trjconv commands.

_____


.. class:: infomark

**Input**

       - One or more trajectory file (XTC or TRR)
       - Structure file (optional)
       - Various options can be set

_____

        
.. class:: infomark

**Output**

       - GROMACS trajectory or structure file (XTC, TRR, PDB, GRO)


    ]]></help>
    <expand macro="citations" />
</tool>