diff rdconf.xml @ 0:5c501eb8d56c draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rdconf.xml	Sat Dec 04 16:39:31 2021 +0000
@@ -0,0 +1,99 @@
+<tool id="rdconf" name="RDConf: Low-energy ligand conformer search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>using RDKit</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2020.03.4</token>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+      <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/rdconf.py'
+            '$infile'
+            --maxconfs '$CNT'
+            --sample_multiplier '$N'
+            --seed '$s'
+            --rms_threshold '$R'
+            --energy_window '$E'
+            $mmff
+            $nomin
+            $etkdg
+            '$outfile'
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="smi" label="Input file" help="Input file in SMILES format."/>
+        <param name="CNT" type="integer"  value="20" label="Maximum number of conformers to generate per molecule"/>
+        <param name="N" type="integer" value="1" label="Sample an integer multiple of the maximum conformer value and choose the conformers with lowest energy"/>
+        <param name="s" type="integer" value="9162006" label="Random seed"/>
+        <param name="R" type="float" value="0.7" min="0" label="RMSD threshold" help="If a conformer is too similar to those already generated (below the RMSD threshold), it is discarded and regenerated."/>
+        <param name="E" type="float" value="10" label="Energy window threshold (kcal/mol)."/>
+        <param name="mmff" type="boolean" value="" truevalue="--mmff" falsevalue="" label="Use MMFF forcefield (default UFF)"/>
+        <param name="nomin" type="boolean" value="" truevalue="--nomin" falsevalue="" label="Skip minimization" help="Not recommended"/>
+        <param name="etkdg" type="boolean" value="" truevalue="--etkdg" falsevalue="" label="Use new ETKDG knowledge-based method (default distance geometry)"/>
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="sdf" label="Output for ${tool.name}"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="infile" value="staurosporine.smi" ftype="smi"/>
+            <param name="CNT" value="100"/>
+            <param name="N" value="1"/>
+            <param name="s" value="100"/>
+            <param name="R" value="0.7"/>
+            <param name="E" value="10"/>                       
+            <param name="mmff" value="--mmff" />
+            <param name="nomin" value="--nomin" />
+            <param name="etkdg" value="--etkdg" />
+            <output name="outfile" ftype="sdf" file="rdconf_output.sdf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+
+This tool generates low-energy conformers for a set of input molecules, using the chemistry toolkit RDKit. It is based on a script written by David Koes.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+| - Molecules in `SMI format`_
+| - A number of other parameters can be set; the most important include the number of conformers (default 20) to generate and the minimum RMSD difference (default 0.7) between them.
+
+.. _SMI format: https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+`SD-file`_ containing generated conformers.
+
+.. _SD-file: http://en.wikipedia.org/wiki/Chemical_table_file
+
+]]></help>
+    <citations>
+        <citation type="bibtex">
+            @article{rdkit,
+                author = {Greg Landrum and others},
+                title = {RDKit: Open-source cheminformatics},
+                url ={http://www.rdkit.org}
+            }</citation>
+                    <citation type="bibtex">
+            @article{rdconf,
+                author = {David Koes},
+                title = {RDConf: Low-energy ligand conformer search},
+                url ={https://github.com/dkoes/rdkit-scripts}
+            }</citation>
+    </citations>
+</tool>
+