diff openduck_chunk.xml @ 0:89c3bd4f50a3 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/openduck_chunk.xml	Thu Apr 16 08:25:04 2020 -0400
@@ -0,0 +1,85 @@
+<tool id="openduck_chunk" name="OpenDUck chunk" version="@VERSION@">
+    <description>for dynamic undocking</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        cp '$ligand' ./ligand.sdf &&
+        duck_chunk
+            -p '$protein'
+            -l ./ligand.sdf
+            -c '$cutoff'
+            $ignore_buffers
+            ## -i is interaction, e.g. A_ASP_156_OD2
+            -i '${ia.chain_sel}'_'${ia.res_sel}'_'${ia.resid_sel}'_'${ia.atom_sel}'
+
+        #if $return_tar:
+            && tar -czf allfiles.tar.gz --exclude=allfiles.tar.gz *
+        #end if
+
+    ]]></command>
+    <inputs>
+        <param argument="protein" type="data" format='pdb' label="PDB file for apoprotein"/>
+        <param argument="ligand" type="data" format='sdf,mol' label="SDF/MOL file containing a single ligand"/>
+        <param argument="cutoff" type="float" min="0" value="5" label="Cutoff" help="Cutoff for chunk generation (in angstroms)" />
+        <param argument="ignore_buffers" type="select" label="Ignore buffers (solvent, ions etc.)?">
+            <option value="">Remove buffers</option>
+            <option value="-b">Leave buffers</option>
+        </param>
+        <expand macro="interaction_params" />
+        <expand macro="tar_param" />
+
+    </inputs>
+    <outputs>
+        <data name="chunk" format="pdb" from_work_dir="protein_out_prot.pdb" label="${tool.name} PDB file"/>
+        <expand macro="tar_output" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="protein" value="1n2v_apo.pdb" />
+            <param name="ligand" value="ligand.mol" />
+            <param name="cutoff" value="5" />
+            <param name="ignore_buffers" value="" />
+            <param name="chain_sel" value="A" />
+            <param name="res_sel" value="ASP" />
+            <param name="resid_sel" value="156" />
+            <param name="atom_sel" value="OD2" />
+            <param name="return_tar" value="false" />
+            <output name="chunk" file="protein_out_prot.pdb" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Produce chunk automatically for dynamic undocking (DUck). Chunking entails selecting a region of the protein which is used for a DUck simulation.
+
+This Galaxy tool uses OpenDUck, an open-source implementation of the original DUck method, using OpenMM and AmberTools.
+
+_____
+
+.. class:: infomark
+
+**Input**
+
+       - PDB file for protein
+       - SDF/MOL file for ligand
+       - Parameters defining the protein-ligand interaction
+
+_____
+
+        
+.. class:: infomark
+
+**Output**
+
+       - PDB file containing the chunked protein ready for system preparation.
+
+A tar file is also produced as a optional output, containing all files produced by the tool.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
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