| Previous changeset 1:ddb1ae2cf028 (2019-08-30) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" |
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modified:
macros_packmol.xml packmol.xml template.j2 |
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| diff -r ddb1ae2cf028 -r 539fb45630e6 macros_packmol.xml --- a/macros_packmol.xml Fri Aug 30 15:02:54 2019 -0400 +++ b/macros_packmol.xml Mon Oct 07 12:46:54 2019 -0400 |
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| @@ -3,12 +3,12 @@ <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):"> <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/> <section name="structureparams" title="Structure Parameters (Make Changes!)" expanded="false"> - <param name="number" type="integer" multiple="True" value="100" /> - <param name="radius" type="float" multiple="True" value="1.0" /> - <param name="resnumbers" type="integer" multiple="True" value="0" help="Default is to number 1 to n for type 1 and 1 to n for type 2"/> + <param name="number" label="Number" type="integer" multiple="True" value="100" help="How many molecules to create"/> + <param name="radius" label="Radius" type="float" multiple="True" value="1.0" help="Molecular radius (angstroms)"/> + <param name="resnumbers" label="Resnumbers" type="integer" multiple="True" value="0" help="Default is to number 1 to n for type 1 and 1 to n for type 2"/> <repeat name="constraints_repeat" min="1" max="3" title="Select constraint(s) to apply:"> <conditional name="constraints"> - <param name="constraint" type="select" label="Shape Constraint selection" help="Choose the constraint for the molecules"> + <param name="constraint" type="select" label="Shape constraint selection" help="Choose the constraint for the molecules"> <option value="fixed">fixed - hold 1 molecule in fixed position (hardcoded number=1) Exclusive other constraints not possible</option> <option selected="True" value="cube">cube</option> <option value="box">box</option> |
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| diff -r ddb1ae2cf028 -r 539fb45630e6 packmol.xml --- a/packmol.xml Fri Aug 30 15:02:54 2019 -0400 +++ b/packmol.xml Mon Oct 07 12:46:54 2019 -0400 |
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| @@ -1,5 +1,5 @@ -<tool id="packmol" name="PACKMOL" version="18.169"> - <description>Initial configurations for Molecular Dynamics simulations by packing optimization</description> +<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> @@ -27,12 +27,12 @@ # get the inputs input_iter = [] -#for $i, $s in enumerate( $packmol_format.packmol_inputs ) +#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_format"]["packmol_inputs"][pmfile_index]["file"] = pmfile_path -params["packmol_format"]["packmol_inputs"][pmfile_index]["datasetname"] = "${s.input.name}" +params["packmol_inputs"][pmfile_index]["file"] = pmfile_path ## params["packmol_format"]["packmol_inputs"] +params["packmol_inputs"][pmfile_index]["datasetname"] = "${s.input.name}" ## params["packmol_format"]["packmol_inputs"] #end for params["outfile"] = "$outfile" @@ -49,17 +49,18 @@ </configfile> </configfiles> <inputs> - <conditional name="packmol_format"> + + <!-- <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="xyz">xyz</option> <option value="tinker">tinker</option> - <option value="moldy">moldy</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"> + <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"> @@ -67,23 +68,24 @@ </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" /> + </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> + <!-- <change_format> <when input="selected_format" value="pdb" format="pdb"/> - <!-- <when input="selected_format" value="xyz" format="xyz"/> + <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> + <when input="selected_format" value="moldy" format="moldy"/> + </change_format> --> </data> <data format="txt" name="parameteroutfile" label="${tool.name}: parameter output"/> </outputs> @@ -128,14 +130,14 @@ **What it does** -Packmol creates initial MD configurations from input molecules. For example, create a water and urea mixture. +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 single molecule from your history (can select multiple) +- 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: @@ -149,7 +151,7 @@ **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 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 @@ -163,7 +165,7 @@ **Known issues** -- fixed constraint only allows 1 atom but this is not set for the user. user has to set this. Job may fail. +- 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 |
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| diff -r ddb1ae2cf028 -r 539fb45630e6 template.j2 --- a/template.j2 Fri Aug 30 15:02:54 2019 -0400 +++ b/template.j2 Mon Oct 07 12:46:54 2019 -0400 |
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| @@ -5,10 +5,10 @@ nloop {{ allparams.nloop }} maxit {{ allparams.maxit }} seed {{ allparams.seed }} -filetype {{packmol_format.selected_format}} +filetype pdb output {{outfile}} -{% for struct in packmol_format.packmol_inputs %} +{% for struct in packmol_inputs %} structure {{struct.file}} # Galaxy datasetname - {{struct.datasetname}} number {{struct.structureparams.number}} |