# HG changeset patch
# User fmercuri
# Date 1624483672 0
# Node ID db62543db01a6e3d180c83f144e9e25bda08cd54

Uploaded

diff -r 000000000000 -r db62543db01a packmol.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/packmol.xml	Wed Jun 23 21:27:52 2021 +0000
@@ -0,0 +1,178 @@
+<tool id="packmol_daimoners" name="PACKMOL daimoners version" 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>
+    </requirements>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        python3 '$packmol_script' '$inputs' &&
+        packmol < '$parameteroutfile'
+        ]]>
+    </command>
+    <configfiles>
+        <inputs name="inputs" />
+        <configfile name="packmol_script"><![CDATA[
+
+import os
+import sys
+import json
+
+from jinja2 import Environment, FileSystemLoader
+
+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 = "$__tool_directory__"  # should work generally
+template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)
+template = template_environment.get_template('template.j2')
+print(params)
+
+with open("$parameteroutfile",'w+') as f:
+    f.write(template.render(params))
+
+]]>
+        </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>
+            <param name="selected_format" value="pdb"/>
+            <param name="packmol_inputs_0|input" value="water.pdb" ftype="pdb"/>
+            <param name="allparams.seed" value="101"/>
+            <output name="outfile" file="packmol_outfile1.pdb" compare="sim_size" delta="100000">
+                <assert_contents>
+                    <has_text text="HETATM  300  O   HOH"/>
+                </assert_contents>
+            </output>
+            <output name="parameteroutfile" file="packmol_parameteroutfile_1.txt" compare="diff" lines_diff="6"/>
+        </test>
+        <test>
+            <param name="selected_format" value="pdb"/>
+            <param name="packmol_inputs_0|input" value="water.pdb" ftype="pdb"/>
+            <param name="packmol_inputs_1|input" value="urea.pdb" ftype="pdb"/>
+            <param name="packmol_inputs_0|structureparams|number" value="1000"/>
+            <param name="packmol_inputs_1|structureparams|number" value="400"/>
+            <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|constraint" value="box"/>
+            <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|xmax" value="40.0"/>
+            <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|ymax" value="40.0"/>
+            <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|zmax" value="40.0"/>
+            <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|constraint" value="box"/>
+            <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|xmax" value="40.0"/>
+            <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|ymax" value="40.0"/>
+            <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|zmax" value="40.0"/>
+            <param name="allparams.seed" value="-1"/>
+            <output name="outfile" file="packmol_outfile2.pdb" compare="sim_size" delta="100000">
+                <assert_contents>
+                    <has_text text="HETATM 3000  O   HOH"/>
+                    <has_text text="HETATM 6200  H     2 B"/>
+                </assert_contents>
+            </output>
+            <output name="parameteroutfile" file="packmol_parameteroutfile_2.txt" compare="diff" lines_diff="6"/>
+        </test>
+    </tests>
+    <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)
+   - choose one or more placement constraint(s). Each constraint has different parameters:
+       - for example, specify placement inside a cube of size 40 Angstroms placed at the origin
+       - all units are in Angstroms for distances and degrees for angles
+
+.. 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**
+
+- Packmol `userguide`_
+- Calculating the number of molecules using the `volume guesser`_
+
+.. 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
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1002/jcc.21224</citation>
+    </citations>
+</tool>