diff openduck_run_smd.xml @ 0:05c95b16823b 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_run_smd.xml	Thu Apr 16 08:25:46 2020 -0400
@@ -0,0 +1,107 @@
+<tool id="openduck_run_smd" name="Run OpenDUck" version="@VERSION@">
+    <description>steered molecular dynamics runs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ## to run on GPU set OPENDUCK_GPU_PARAM to something like "--gpu-id 1"
+        cp '$ligand' ./ligand.sdf &&
+        
+        duck_prepare_sys
+            -p '$protein'
+            -l ./ligand.sdf
+            -c '$chunk'
+            ## -i is interaction, e.g. A_ASP_156_OD2
+            -i '${ia.chain_sel}'_'${ia.res_sel}'_'${ia.resid_sel}'_'${ia.atom_sel}' 
+            \${OPENDUCK_GPU_PARAM} &&
+
+        mv equil.chk eql.chk &&
+        mv complex_system.pickle cs.pickle &&
+
+        duck_smd_runs
+            -i eql.chk
+            -p cs.pickle
+            -n '$num'
+            -l '$mdlen'
+            -d '$start_dist'
+            -v '$vel'
+            \${OPENDUCK_GPU_PARAM} &&
+        #if $return_tar:
+            tar -czf allfiles.tar.gz --exclude=allfiles.tar.gz * &&
+        #end if
+        get_wqb -l '$ligand' -o '$ligand_wqb'
+    ]]></command>
+    <inputs>
+        <param argument="protein" type="data" format='pdb' label="PDB file for apoprotein"/>
+        <param argument="chunk" type="data" format='pdb' label="Chunk (in PDB format)" help="PDB file produced by chunk tool."/>
+        <param argument="ligand" type="data" format='sdf,mol' label="SDF/MOL file containing a single ligand"/>
+        <expand macro="interaction_params" />
+        <param argument="mdlen" type="float" min="0" value="0.05" label="MD run length (ns)" help="Length of initial MD run (prior to steered molecular dynamics runs)."/>
+        <param argument="start_dist" type="float" min="0" value="2.5" label="Starting distance" help="Initial length of the selected interaction between protein and ligand."/>
+        <param argument="num" type="integer" min="0" value="1" label="Number of SMD runs" help="Number of steered molecular dynamics runs to perform."/>
+        <param argument="vel" type="float" min="0" value="0.00001" label="Velocity" help="Distance (in angstroms) to perturb the system per simulation step in the SMD runs. Decreasing this value will increase simulation time."/>
+        <expand macro="tar_param" />
+    </inputs>
+    <outputs>
+        <data name="ligand_wqb" format="sdf" label="SD-file with DUck score"/>
+        <expand macro="tar_output" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="protein" value="1n2v_apo.pdb" />
+            <param name="ligand" value="ligand.mol" />
+            <param name="chunk" value="protein_out_prot.pdb" />
+            <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="num" value="1" />
+            <param name="mdlen" value="0.05" />
+            <param name="start_dist" value="2.5" />
+            <param name="vel" value="0.00001" />
+            <output name="ligand_wqb" file="ligand_wqb.mol" lines_diff="2" />
+            <output name="tar" >
+                <assert_contents>
+                    <has_size value="6718500" delta="500"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Perform steered molecular dynamics runs for dynamic undocking (DUck), performing system preparation (topology calculation and minimization), an initial MD run, and SMD runs.
+
+This Galaxy tool uses OpenDUck, an open-source implementation of the original DUck method, using OpenMM and AmberTools.
+
+_____
+
+.. class:: infomark
+
+**Input**
+
+       - PDB file for apoprotein
+       - PDB file for chunk
+       - SDF/MOL file for ligand
+       - Parameters defining the protein-ligand interaction
+       - Parameters for MD and SMD runs
+
+_____
+
+
+.. class:: infomark
+
+**Output**
+
+       - Ligand in SDF/MOL format, with added `<SCORE.DUCK_WQB>` parameter.
+
+A tar file is also produced as a optional output, containing all files produced by the tool.
+
+    ]]></help>
+
+    <expand macro="citations" />
+</tool>