comparison packmol.xml @ 2:9d1e7348f7a8 draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"

1:090546cfd52c

<tool id="packmol" name="PACKMOL" version="18.169">
    <description>Initial configurations for Molecular Dynamics simulations by packing optimization</description>
    <macros>
        <import>macros_packmol.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="18.169">packmol</requirement>

input_json_path = sys.argv[1]
params = json.load(open(input_json_path, "r"))

# get the inputs
input_iter = []
#for $i, $s in enumerate( $packmol_format.packmol_inputs )
pmfile_index = $i
pmfile_path = "${s.input.file_name}"
input_iter.append(pmfile_path)
params["packmol_format"]["packmol_inputs"][pmfile_index]["file"] = pmfile_path
params["packmol_format"]["packmol_inputs"][pmfile_index]["datasetname"] = "${s.input.name}"
#end for

params["outfile"] = "$outfile"

currentpath = "$__tool_directory__"  # should work generally

]]>
        </configfile>
    </configfiles>
    <inputs>
        <conditional name="packmol_format">
            <param name="selected_format" type="select" label="Select a file format:">
                <option value="pdb" selected="true">pdb</option>
                <!--option value="xyz">xyz</option>
                <option value="tinker">tinker</option>
                <option value="moldy">moldy</option-->
            </param>
            <when value="pdb">
                <expand macro="multiple_input" name="packmol_inputs" format="pdb" label="pdb input with molecule type" help_text="Select a pdb file in .pdb format"/>
            </when>
            <!--when value="xyz">
                <expand macro="multiple_input" name="packmol_inputs" format="xyz" label="xyz input with molecule type" help_text="Select a xyz file in .xyz format"/>
            </when>
            <when value="tinker">
                <expand macro="multiple_input" name="packmol_inputs" format="tinker" label="tinker input with molecule type" help_text="Select a tinker file in .tinker format"/>
            </when>
            <when value="moldy">
                <expand macro="multiple_input" name="packmol_inputs" format="moldy" label="moldy input with molecule type" help_text="Select a moldy file in .moldy format"/>
            </when-->
        </conditional>
        <section name="allparams" title="General Parameters" expanded="false">
            <param name="tolerance" type="float" value="2.0" label="distance tolerance" min="0.0" max="100.0"/>
            <param name="nloop" type="integer" value="20" label="maximum number of optimisation loops" min="1" max="10000"/>
            <param name="maxit" type="integer" value="20" label="maximum number of gencan iterations per loop" min="1" max="10000"/>
            <param name="seed" type="integer" value="-1" label="random number generator seed, default of -1 used the computer time to set the seed" />
        </section>
    </inputs>
    <outputs>
        <data format="pdb" name="outfile" label="${tool.name}: structure output">
        <change_format>
            <when input="selected_format" value="pdb" format="pdb"/>
            <!-- <when input="selected_format" value="xyz" format="xyz"/>
            <when input="selected_format" value="tinker" format="tinker"/>
            <when input="selected_format" value="moldy" format="moldy"/> -->
        </change_format>
        </data>
        <data format="txt" name="parameteroutfile" label="${tool.name}: parameter output"/>
    </outputs>
    <tests>
        <test>

    <help><![CDATA[
.. class:: infomark

**What it does**

Packmol creates initial MD configurations from input molecules. For example, create a water and urea mixture.

.. class:: infomark

**How it works**

- Select a molecule file type e.g. pdb,xyz
- Select single molecule from your history (can select multiple)
- For each molecule:
   - choose how many molecules to create (number variable)
   - optionally choose:
       - molecular radius
       - how to number the molecules (resnumber variable)

.. class:: infomark

**Outputs created**

- A pdb file, view this in Galaxy by clicking on visualise and choosing a viewer. The NGLViewer works well for small molecules.
- A packmol input script (for debugging and repeatability)

.. class:: infomark

**User guide and documentation**

.. class:: infomark

**Known issues**

- fixed constraint only allows 1 atom but this is not set for the user. user has to set this. Job may fail.

.. _`userguide`: http://m3g.iqm.unicamp.br/packmol/userguide.shtml#more
.. _`volume guesser`: http://m3g.iqm.unicamp.br/packmol/utilities.shtml

]]>

2:9d1e7348f7a8

<tool id="packmol" name="PACKMOL" version="18.169.1">
    <description>- initial configurations for molecular dynamics simulations by packing optimization</description>
    <macros>
        <import>macros_packmol.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="18.169">packmol</requirement>

input_json_path = sys.argv[1]
params = json.load(open(input_json_path, "r"))

# get the inputs
input_iter = []
#for $i, $s in enumerate( $packmol_inputs )  ## enumerate( $packmol_format.packmol_inputs )
pmfile_index = $i
pmfile_path = "${s.input.file_name}"
input_iter.append(pmfile_path)
params["packmol_inputs"][pmfile_index]["file"] = pmfile_path  ## params["packmol_format"]["packmol_inputs"]
params["packmol_inputs"][pmfile_index]["datasetname"] = "${s.input.name}"  ## params["packmol_format"]["packmol_inputs"]
#end for

params["outfile"] = "$outfile"

currentpath = "$__tool_directory__"  # should work generally

]]>
        </configfile>
    </configfiles>
    <inputs>

        <!-- <conditional name="packmol_format">
            <param name="selected_format" type="select" label="Select a file format:">
                <option value="pdb" selected="true">pdb</option>
                <option value="xyz">xyz</option>
                <option value="tinker">tinker</option>
                <option value="moldy">moldy</option>
            </param>
            <when value="pdb">
                <expand macro="multiple_input" name="packmol_inputs" format="pdb" label="pdb input with molecule type" help_text="Select a pdb file in .pdb format"/>
            </when>
            <when value="xyz">
                <expand macro="multiple_input" name="packmol_inputs" format="xyz" label="xyz input with molecule type" help_text="Select a xyz file in .xyz format"/>
            </when>
            <when value="tinker">
                <expand macro="multiple_input" name="packmol_inputs" format="tinker" label="tinker input with molecule type" help_text="Select a tinker file in .tinker format"/>
            </when>
            <when value="moldy">
                <expand macro="multiple_input" name="packmol_inputs" format="moldy" label="moldy input with molecule type" help_text="Select a moldy file in .moldy format"/>
            </when>
        </conditional> -->
        <expand macro="multiple_input" name="packmol_inputs" format="pdb" label="PDB input with molecule type" help_text="Select a PDB file in .pdb format"/>
        <section name="allparams" title="General parameters" expanded="false">
            <param name="tolerance" type="float" value="2.0" label="Distance tolerance" min="0.0" max="100.0"/>
            <param name="nloop" type="integer" value="20" label="Maximum number of optimisation loops" min="1" max="10000"/>
            <param name="maxit" type="integer" value="20" label="Maximum number of gencan iterations per loop" min="1" max="10000"/>
            <param name="seed" type="integer" value="-1" label="Random number generator seed, default of -1 uses the computer time to set the seed" />
        </section>
    </inputs>
    <outputs>
        <data format="pdb" name="outfile" label="${tool.name}: structure output">
        <!-- <change_format>
            <when input="selected_format" value="pdb" format="pdb"/>
            <when input="selected_format" value="xyz" format="xyz"/>
            <when input="selected_format" value="tinker" format="tinker"/>
            <when input="selected_format" value="moldy" format="moldy"/>
        </change_format> -->
        </data>
        <data format="txt" name="parameteroutfile" label="${tool.name}: parameter output"/>
    </outputs>
    <tests>
        <test>

    <help><![CDATA[
.. class:: infomark

**What it does**

Packmol creates initial MD configurations from input molecules - for example, creating a water and urea mixture.

.. class:: infomark

**How it works**

- Select a molecule file type e.g. pdb, xyz
- Select a single molecule from your history (can select multiple)
- For each molecule:
   - choose how many molecules to create (number variable)
   - optionally choose:
       - molecular radius
       - how to number the molecules (resnumber variable)

.. class:: infomark

**Outputs created**

- A pdb file; view this in Galaxy by clicking on the 'visualize' icon and choosing a viewer. The NGLViewer works well for small molecules.
- A packmol input script (for debugging and repeatability)

.. class:: infomark

**User guide and documentation**

.. class:: infomark

**Known issues**

- fixed constraint only allows 1 atom but this is not set for the user. The user has to set this parameter. The job may fail.

.. _`userguide`: http://m3g.iqm.unicamp.br/packmol/userguide.shtml#more
.. _`volume guesser`: http://m3g.iqm.unicamp.br/packmol/utilities.shtml

]]>