comparison trj.xml @ 4:9363254ef848 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"

3:6ac5f450ad31

<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[

            <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="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

4:9363254ef848

<tool id="gmx_trj" name="Modify/convert GROMACS trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>using trjconv and trjcat</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>

    <expand macro="requirements" />

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

            <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="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