comparison sim.xml @ 9:6398e0b14e0e draft default tip

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

8:5bc9383b1955

<tool id="gmx_sim" name="GROMACS simulation" version="@VERSION@.1">
    <description>for system equilibration or data collection</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #if $sets.mdp.mdpfile == "custom":
            ln -s '$sets.mdp.mdp_input' ./md.mdp &&

            #end if
            -p ./top_input.top 
            -o outp.tpr &>> verbose.txt &&


        gmx mdrun -nt "\${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt
 
        #if $outps.str == 'pdb' or $outps.str == 'both'
            && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt
        #end if

        && cat md.mdp &>> verbose.txt

        <expand macro="log_outputs" />
    </outputs>

    <tests>
        <test expect_num_outputs="3">
            <param name="gro_input" value="npt.gro" />
            <param name="top_input" value="topol_solv.top" />
            <!-- <param name="cpt_bool" value="yes" /> -->
            <param name="cpt_in" value="npt.cpt" />
            <param name="mdpfile" value="custom" />
            <param name="mdp_input" value="md.mdp" />

            <param name="traj" value="trr"/>
            <param name="str" value="gro"/>
            <param name="tpr_out" value="true"/>
            <param name="ensemble" value="npt" />
            <!-- <param name="posres_bool" value="false" /> -->
            <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
            <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
            <output name="output8" file="md_0_1.tpr" ftype="binary" compare="sim_size"/>
            <!-- <output name="output1" ftype="gro">
                <assert_contents>
                    <has_size value="2647999" />
                </assert_contents>
            </output>
            <output name="output3" ftype="trr">
                <assert_contents>
                    <has_size value="10132584" />
                </assert_contents>
            </output> -->
        </test>

        <test expect_num_outputs="3">
            <param name="gro_input" value="npt.gro" />
            <param name="top_input" value="topol_solv.top" />
            <!-- <param name="cpt_bool" value="yes" /> -->
            <param name="cpt_in" value="npt.cpt" />
            <!-- <param name="ndx_bool" value="false" /> -->
            <param name="traj" value="trr"/>
            <param name="str" value="both"/>
            <expand macro="test_params"/>
            <param name="ensemble" value="npt" />
            <!-- <param name="posres_bool" value="false" /> -->
            <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
            <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>
            <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
        </test>

        <test expect_num_outputs="3">
            <param name="gro_input" value="npt.gro" />
            <param name="top_input" value="topol_solv.top" />
            <!-- <param name="cpt_bool" value="yes" /> -->
            <param name="cpt_in" value="npt.cpt" />
            <!-- <param name="ndx_bool" value="true" /> -->
            <param name="ndx_in" value="index.ndx" />
            <param name="traj" value="trr"/>
            <param name="str" value="both"/>
            <expand macro="test_params"/>
            <param name="ensemble" value="npt" />
            <!-- <param name="posres_bool" value="false" /> -->
            <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
            <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>
            <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
        </test>

        <test expect_num_outputs="3">
            <param name="gro_input" value="em.gro" />
            <param name="top_input" value="topol_solv.top" />
            <!-- <param name="posres_bool" value="true" /> -->
            <param name="itp_in" value="posres.itp" />
            <!-- <param name="cpt_bool" value="no" /> -->
            <param name="cpt_out" value="true" />

            <param name="traj" value="xtc"/>
            <param name="str" value="pdb"/>
            <param name="ensemble" value="nvt" />
            <expand macro="test_params"/>
            
            <output name="output2" file="nvt.pdb" ftype="pdb" compare="sim_size"/>
            <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/>
            <output name="output5" file="nvt.cpt" ftype="cpt" compare="sim_size"/>
        </test>
    </tests>
    
    <help><![CDATA[

9:6398e0b14e0e

<tool id="gmx_sim" name="GROMACS simulation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>for system equilibration or data collection</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #if $sets.mdp.mdpfile == "custom":
            ln -s '$sets.mdp.mdp_input' ./md.mdp &&

            #end if
            -p ./top_input.top 
            -o outp.tpr &>> verbose.txt &&


        gmx mdrun
            -nt "\${GALAXY_SLOTS:-4}"
            ## GPU
            #if "\${GROMACS_GPU:-0}" == 1:
                -ntmpi 1
                -nb gpu
                -pme gpu
            #end if
            -deffnm outp &>> verbose.txt

        #if $outps.str == 'pdb' or $outps.str == 'both'
            && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt
        #end if

        && cat md.mdp &>> verbose.txt

        <expand macro="log_outputs" />
    </outputs>

    <tests>
        <test expect_num_outputs="3">
            <param name="gro_input" value="str_ions.gro" />
            <param name="top_input" value="topol_solv.top" />
            <!-- <param name="cpt_bool" value="yes" /> -->
            <param name="cpt_in" value="npt.cpt" />
            <param name="mdpfile" value="custom" />
            <param name="mdp_input" value="md.mdp" />

            <param name="traj" value="trr"/>
            <param name="str" value="gro"/>
            <param name="tpr_out" value="true"/>
            <param name="ensemble" value="npt" />
            <!-- <param name="posres_bool" value="false" /> -->
            <output name="output1" ftype="gro">
                <assert_contents>
                    <has_size value="6537" />
                    <has_n_lines n="97" />
                    <has_line line="TEST in water" />
                </assert_contents>
            </output>
            <output name="output3" ftype="trr">
                <assert_contents>
                    <has_size value="26136" />
                </assert_contents>
            </output>
            <output name="output8" ftype="binary">
                <assert_contents>
                    <has_size value="44164" />
                </assert_contents>
            </output>
        </test>

        <test expect_num_outputs="3">
            <param name="gro_input" value="str_ions.gro" />
            <param name="top_input" value="topol_solv.top" />
            <!-- <param name="cpt_bool" value="yes" /> -->
            <param name="cpt_in" value="npt.cpt" />
            <!-- <param name="ndx_bool" value="false" /> -->
            <param name="traj" value="trr"/>
            <param name="str" value="both"/>
            <expand macro="test_params"/>
            <param name="ensemble" value="npt" />
            <!-- <param name="posres_bool" value="false" /> -->
            <output name="output1" ftype="gro">
                <assert_contents>
                    <has_size value="6537" />
                    <has_n_lines n="97" />
                    <has_line line="TEST in water" />
                </assert_contents>
            </output>            
            <output name="output2" ftype="pdb">
                <assert_contents>
                    <has_size value="7582" />
                    <has_n_lines n="100" />
                    <has_line line="TITLE     TEST in water" />
                    <has_line line="REMARK    THIS IS A SIMULATION BOX" />
                </assert_contents>
            </output>
            <output name="output3" ftype="trr">
                <assert_contents>
                    <has_size value="26136" />
                </assert_contents>
            </output>
        </test>

        <test expect_num_outputs="3">
            <param name="gro_input" value="str_ions.gro" />
            <param name="top_input" value="topol_solv.top" />
            <!-- <param name="cpt_bool" value="yes" /> -->
            <param name="cpt_in" value="npt.cpt" />
            <!-- <param name="ndx_bool" value="true" /> -->
            <param name="ndx_in" value="index.ndx" />
            <param name="traj" value="trr"/>
            <param name="str" value="both"/>
            <expand macro="test_params"/>
            <param name="ensemble" value="npt" />
            <!-- <param name="posres_bool" value="false" /> -->
            <output name="output1" ftype="gro" compare="sim_size">
                <assert_contents>
                    <has_size value="6537" />
                    <has_n_lines n="97" />
                    <has_line line="TEST in water" />
                </assert_contents>
            </output>
            <output name="output2" ftype="pdb" compare="sim_size">
                <assert_contents>
                    <has_size value="7582" />
                    <has_n_lines n="100" />
                    <has_line line="TITLE     TEST in water" />
                    <has_line line="REMARK    THIS IS A SIMULATION BOX" />
                </assert_contents>
            </output>
            <output name="output3" ftype="trr" compare="sim_size">
                <assert_contents>
                    <has_size value="26136" />
                </assert_contents>
            </output>
        </test>

        <test expect_num_outputs="3">
            <param name="gro_input" value="str_ions.gro" />
            <param name="top_input" value="topol_solv.top" />
            <!-- <param name="posres_bool" value="true" /> -->
            <param name="itp_in" value="posres.itp" />
            <!-- <param name="cpt_bool" value="no" /> -->
            <param name="cpt_out" value="true" />

            <param name="traj" value="xtc"/>
            <param name="str" value="pdb"/>
            <param name="ensemble" value="nvt" />
            <expand macro="test_params"/>
            
            <output name="output2" ftype="pdb">
                <assert_contents>
                    <has_size value="7582" />
                    <has_n_lines n="100" />
                    <has_line line="TITLE     TEST in water" />
                    <has_line line="REMARK    THIS IS A SIMULATION BOX" />
                </assert_contents>
            </output>
            <output name="output4" ftype="xtc">
                <assert_contents>
                    <has_size value="4910" delta="20"/>
                </assert_contents>
            </output>
            <output name="output5" ftype="cpt">
                <assert_contents>
                    <has_size value="3350"  delta="20"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[