diff smina.xml @ 0:bc03dbb6eb37 draft

planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smina.xml	Mon Aug 29 03:38:13 2016 -0400
@@ -0,0 +1,148 @@
+<tool id="smina" name="smina" version="0.1.0">
+    <requirements>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+        <![CDATA[ 
+        cat $receptor > receptor.pdbqt;
+        cat $ligand > ligand.pdbqt;
+        $__tool_directory__/tools/smina/smina.static 
+                                                    --receptor receptor.pdbqt 
+                                                    --ligand ligand.pdbqt 
+
+                                                    #if $flex
+                                                    --flex $flex
+                                                    #end if
+                                                    #if $flexres
+                                                    --flexres $flexres
+                                                    #end if
+                                                    #if $flexdist_ligand
+                                                    --flexdist_ligand $flexdist_ligand
+                                                    #end if
+                                                    #if $flexdist
+                                                    --flexdist $flexdist
+                                                    #end if
+
+                                                    --center_x $center_x 
+                                                    --center_y $center_y
+                                                    --center_z $center_z 
+                                                    --size_x $size_x
+                                                    --size_y $size_y
+                                                    --size_z $size_z
+
+                                                    #if $autobox_ligand
+                                                    --autobox_ligand $autobox_ligand 
+                                                    #end if 
+                                                    #if $autobox_add 
+                                                    --autobox_add $autobox_add
+                                                    #end if
+                                                    #if $no_lig=="true"
+                                                    --no_lig
+                                                    #end if 
+
+                                                    --scoring $scoring 
+                                                    #if $custom_scoring
+                                                    --custom_scoring $custom_scoring
+                                                    #end if
+                                                    #if $custom_atoms
+                                                    --custom_atoms $custom_atoms 
+                                                    #end if
+                                                    #if $score_only=="true"
+                                                    --score_only 
+                                                    #end if
+                                                    #if $local_only=="true"
+                                                    --local_only 
+                                                    #end if
+                                                    #if $minimize=="true"
+                                                    --minimize 
+                                                    #end if 
+                                                    #if $randomize_only=="true"    
+                                                    --randomize_only  
+                                                    #end if 
+                                                    #if $minimize_iters  
+                                                    --minimize_iters $minimize_iters 
+                                                    #end if
+
+                                                    --seed 1000 > $output;
+                                                    cat $output > /tmp/ouput
+    ]]>
+    </command>
+    <inputs>
+        <param name="receptor" type="data" format="pdbqt" label="receptor: rigid part of the receptore" />
+        <param name="ligand" type="data" format="data" label="ligand: ligand(s)" />
+
+        <param name="flex" type="data" format="pdbqt" label="flex: flexible side chains, if any" optional="true" />
+        <param name="flexres" type="text" label="flexres: flexible side chains specified by comma separated list of chain:resid" optional="true" />
+        <param name="flexdist_ligand" type="data" format="data" label="flexdist_ligand: Ligand to use for flexdist" optional="true" />
+        <param name="flexdist" type="float" label="flexdist: set all side chains within specified distance to flexdist_ligand to flexible" optional="true" />
+
+        <param name="center_x" type="float" value="0" label="center_x: X coordinate of the center" />
+        <param name="center_y" type="float" value="0" label="center_y: Y coordinate of the center" />
+        <param name="center_z" type="float" value="0" label="center_z: Z coordinate of the center" />
+        <param name="size_x" type="integer" value="1" label="size_x: size in the X dimension" />
+        <param name="size_y" type="integer" value="1" label="size_y: size in the Y dimension" />
+        <param name="size_z" type="integer" value="1" label="size_z: size in the Z dimension" />
+
+        <param name="autobox_ligand" type="data" format="data" label="autobox_ligand: Ligand to use for autobox" optional="true" />
+        <param name="autobox_add" type="float" value="4" label="autobox_add: Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" />
+        <param name="no_lig" type="select" label="no_lig: no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" optional="true">
+            <option value="false" selected="true">Don't use this option</option>
+            <option value="true">Use this option</option>
+        </param>
+
+        <param name="scoring" type="select" label="scoring: specify alternative builtin scoring function" optional="true">
+            <option value="default" selected="true">default</option>
+            <option value="ad4_scoring">ad4_scoring</option>
+            <option value="dkoes_fast">dkoes_fast</option>
+            <option value="dkoes_scoring">dkoes_scoring</option>
+            <option value="dkoes_scoring_old">dkoes_scoring_old</option>
+            <option value="vina">vina</option>
+            <option value="vinardo">vinardo</option>
+        </param>
+        <param name="custom_scoring" type="data" format="data" label="custom_scoring: custom scoring function file" optional="true" />
+        <param name="custom_atoms" type="data" format="data" label="custom_atoms: custom atom type parameters file" optional="true" />
+        <param name="score_only" type="select" label="score_only: score provided ligand pose" optional="true">
+            <option value="false" selected="true">Don't use this option</option>
+            <option value="true">Use this option</option>
+            </param>
+        <param name="local_only" type="select" label="local_only: local search only using autobox (you probably want to use --minimize)" optional="true">
+            <option value="false" selected="true">Don't use this option</option>
+            <option value="true">Use this option</option>
+        </param>
+        <param name="minimize" type="select" label="minimize: energy minimization" optional="true">
+            <option value="false" selected="true">Don't use this option</option>
+            <option value="true">Use this option</option>
+        </param>
+        <param name="randomize_only" type="select" label="randomize_only: generate random poses, attempting to avoid clashes" optional="true">
+            <option value="false" selected="true">Don't use this option</option>
+            <option value="true">Use this option</option>
+        </param>
+        <param name="minimize_iters" type="integer" label="minimize_iters: number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" optional="true" />
+    </inputs>
+    <outputs>
+        <data name="output" format="data" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="receptor" value="smina/protein.pdbqt" />
+            <param name="ligand" value="smina/ligand.pdbqt" />
+            <param name="center_x" value="11" />
+            <param name="center_y" value="90.5" />
+            <param name="center_z" value="57.5" />
+            <param name="size_x" value="22" />
+            <param name="size_y" value="24" />
+            <param name="size_z" value="28" />
+            <output name="output" file="smina/output_smina" />
+        </test>
+    </tests>
+    <help>
+        "Smina help"
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{renameTODO, author = {LastTODO, FirstTODO}, year = {TODO}, title = {TODO}, url = {https://sourceforge.net/projects/smina/}, }
+        </citation>
+    </citations>
+</tool>