comparison trj.xml @ 14:72459c3ea5f6 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 033779f5ae0fa964ccad44104027d1d715b8e907"

13:0f2ced72d16f

<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>
        <xml name="fit_when" token_option="none">
            <when value="@OPTION@">
                <param name="index_fit" type="text" label="Index of group to use for fitting" help="Index of group to use for fitting - 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>

    <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

    #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} &&

    echo ## optionally pipe in the following
	#if $trj.fit.fit != 'none':
	    '$trj.fit.index_fit'
    #end if
    #if $trj.pbc.pbc == 'cluster':
	    '$trj.pbc.index_cluster'
    #end if
    '$trj.index_center'	'$trj.index_output' | gmx trjconv
      	-f ./traj.${trj_input.ext}
        -s ./str.${str_input.ext}
        #if $ndx_input:
            -n ./index.ndx
        #end if

                    <expand macro="fit_when" option="transxy"/>
                    <expand macro="fit_when" option="progressive"/>
                </conditional>
            </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"/>
                <param name="sep" type="hidden" value="" />
            </when>
        </conditional>
        <param name="output_format" type="select" label="Output format" >

14:72459c3ea5f6

<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@">1</token>
        <xml name="fit_when" token_option="none">
            <when value="@OPTION@">
                <param name="index_fit" type="text" label="Index of group to use for fitting" help="Index of group to use for fitting - 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>

    <command detect_errors="exit_code"><![CDATA[
    #if $trj.trj_op == 'trjcat':
        mkdir trajs &&
        #for $value, $file in enumerate($trj_input):
            ln -s '$file' trajs/traj_${str(value).rjust(10, '0')}.${file.ext} &&
        #end for

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

    #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} &&

        echo ## optionally pipe in the following
        #if $trj.fit.fit != 'none':
            '$trj.fit.index_fit'
        #end if
        #if $trj.pbc.pbc == 'cluster':
            '$trj.pbc.index_cluster'
        #end if
        '$trj.index_center'	'$trj.index_output' | gmx trjconv
      	-f ./traj.${trj_input.ext}
        -s ./str.${str_input.ext}
        #if $ndx_input:
            -n ./index.ndx
        #end if

                    <expand macro="fit_when" option="transxy"/>
                    <expand macro="fit_when" option="progressive"/>
                </conditional>
            </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 that if you want to take order into account when concatenating, you must use a collection as input." multiple="true"/>
                <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/>
                <param name="sep" type="hidden" value="" />
            </when>
        </conditional>
        <param name="output_format" type="select" label="Output format" >