diff smina.xml @ 0:7c0bb0c48a27 draft default tip

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smina.xml	Tue May 08 19:08:15 2018 -0400
@@ -0,0 +1,197 @@
+<tool id="smina" name="smina" version="1.0">
+    <description>Scoring and Minimization with AutoDock Vina</description>
+    <requirements>
+        <requirement type="package" version="2017.11.9">smina</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+ln -s '$input.receptor' receptor.pdbqt &&
+ln -s '$input.ligand' ligand.pdbqt &&
+smina
+--receptor receptor.pdbqt
+--ligand ligand.pdbqt
+#if $input.flex
+    --flex '$input.flex'
+#end if
+#if $input.flexres
+    --flexres '$input.flexres'
+#end if
+#if $input.flexdist_ligand
+    --flexdist_ligand '$input.flexdist_ligand'
+#end if
+#if str($input.flexdist)
+    --flexdist $input.flexdist
+#end if
+
+--center_x $search_space.center_x
+--center_y $search_space.center_y
+--center_z $search_space.center_z
+--size_x $search_space.size_x
+--size_y $search_space.size_y
+--size_z $search_space.size_z
+#if $search_space.autobox_ligand
+    --autobox_ligand '$search_space.autobox_ligand'
+#end if
+#if str($search_space.autobox_add)
+    --autobox_add $search_space.autobox_add
+#end if
+$search_space.no_lig
+
+--out ligand_out.pdbqt
+#if $output_sect.out_flex
+    --out_flex '$out_flex_output'
+#end if
+#if $output_sect.log
+    --log '$output_log'
+#end if
+#if $output_sect.atom_terms
+    --atom_terms '$atom_terms_output'
+#end if
+$output_sect.atom_term_data
+
+--scoring $scoring_and_minimization.scoring
+#if $scoring_and_minimization.custom_scoring
+    --custom_scoring '$scoring_and_minimization.custom_scoring'
+#end if
+#if $scoring_and_minimization.custom_atoms
+    --custom_atoms '$scoring_and_minimization.custom_atoms'
+#end if
+$scoring_and_minimization.score_only
+$scoring_and_minimization.local_only
+$scoring_and_minimization.minimize
+$scoring_and_minimization.randomize_only
+--minimize_iters $scoring_and_minimization.minimize_iters
+$scoring_and_minimization.accurate_line
+$scoring_and_minimization.minimize_early_term
+#if $scoring_and_minimization.approximation
+    --approximation $scoring_and_minimization.approximation
+#end if
+#if $scoring_and_minimization.factor
+    --factor $scoring_and_minimization.factor
+#end if
+#if str($scoring_and_minimization.force_cap)
+    --force_cap $scoring_and_minimization.force_cap
+#end if
+#if str($scoring_and_minimization.user_grid)
+    --user_grid $scoring_and_minimization.user_grid
+#end if
+--user_grid_lambda $scoring_and_minimization.user_grid_lambda
+$scoring_and_minimization.print_terms
+$scoring_and_minimization.print_atom_types
+
+--cpu \${GALAXY_SLOTS:-1}
+#if str($misc.seed)
+    --seed $misc.seed
+#end if
+--exhaustiveness $misc.exhaustiveness
+--num_modes $misc.num_modes
+--energy_range $misc.energy_range
+--min_rmsd_filter $misc.min_rmsd_filter
+$misc.addH
+    ]]></command>
+    <inputs>
+        <section name="input" title="Input" expanded="True">
+            <param argument="--receptor" type="data" format="pdbqt" label="Rigid part of the receptore" />
+            <param argument="--ligand" type="data" format="pdbqt" label="Ligand(s)" />
+            <param argument="--flex" type="data" format="pdbqt" optional="true" label="Flexible side chains, if any" />
+            <param argument="--flexres" type="text" optional="true" label="Flexible side chains specified by comma separated list of chain:resid" />
+            <param argument="--flexdist_ligand" type="data" format="data" optional="true" label="Ligand to use for flexdist" />
+            <param argument="--flexdist" type="float" optional="true" label="Set all side chains within specified distance to flexdist_ligand to flexible" />
+        </section>
+        <section name="search_space" title="Search space" expanded="True">
+            <param argument="--center_x" type="float" value="0" label="X coordinate of the center" />
+            <param argument="--center_y" type="float" value="0" label="Y coordinate of the center" />
+            <param argument="--center_z" type="float" value="0" label="Z coordinate of the center" />
+            <param argument="--size_x" type="integer" value="1" label="Size in the X dimension" />
+            <param argument="--size_y" type="integer" value="1" label="Size in the Y dimension" />
+            <param argument="--size_z" type="integer" value="1" label="Size in the Z dimension" />
+
+            <param argument="--autobox_ligand" type="data" format="data" optional="true" label="Ligand to use for autobox" />
+            <param argument="--autobox_add" type="float" optional="true" label="Amount of buffer space to add to auto-generated box text" />
+            <param argument="--no_lig" type="boolean" truevalue="--no_lig" falsevalue="" label="No ligand; for sampling/minimizing flexible residues" />
+        </section>
+        <section name="output_sect" title="Output">
+            <param argument="--out_flex" type="boolean" label="Write flexible receptor residues" />
+            <param argument="--log" type="boolean" label="Write log file" />
+            <param argument="--atom_terms" type="boolean" label="Write per-atom interaction term values" />
+            <param argument="--atom_term_data" type="boolean" truevalue="--atom_term_data" falsevalue="" label="Embedded per-atom interaction terms in output sd data" />
+        </section>
+        <section name="scoring_and_minimization" title="Scoring and minimization options">
+            <param argument="--scoring" type="select" label="Specify alternative builtin scoring function">
+                <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 argument="--custom_scoring" type="data" format="data" optional="true" label="Custom scoring function file" />
+            <param argument="--custom_atoms" type="data" format="data" optional="true" label="Custom atom type parameters file" />
+            <param argument="--score_only" type="boolean" truevalue="--score_only" falsevalue="" label="Score provided ligand pose" />
+            <param argument="--local_only" type="boolean" truevalue="--local_only" falsevalue="" label="Local search only using autobox" />
+            <param argument="--minimize" type="boolean" truevalue="--minimize" falsevalue="" label="Energy minimization" />
+            <param argument="--randomize_only" type="boolean" truevalue="--randomize_only" falsevalue="" label="Generate random poses, attempting to avoid clashes" />
+            <param argument="--minimize_iters" type="integer" value="0" label="Number iterations of steepest descent" />
+            <param argument="--accurate_line" type="boolean" truevalue="--accurate_line" falsevalue="" label="Accurate line search" />
+            <param argument="--minimize_early_term" type="boolean" truevalue="--minimize_early_term" falsevalue="" label="Stop minimization before convergence conditions are fully met" />
+            <param argument="--approximation" type="select" optional="true" label="Approximation">
+                <option value="linear">linear</option>
+                <option value="spline">spline</option>
+                <option value="exact">exact</option>
+            </param>
+            <param argument="--factor" type="float" min="0" optional="true" label="Approximation factor: higher results in a finer-grained approximation" />
+            <param argument="--force_cap" type="float" optional="true" label="Max allowed force; lower values more gently minimize clashing structures" />
+            <param argument="--user_grid" type="float" optional="true" label="Autodock map file for user grid data based calculations" />
+            <param argument="--user_grid_lambda" type="float" value="-1" label="Scales user_grid and functional scoring" />
+            <param argument="--print_terms" type="boolean" truevalue="--print_terms" falsevalue="" label="Print all available terms with default parameterizations" />
+            <param argument="--print_atom_types" type="boolean" truevalue="--print_atom_types" falsevalue="" label="Print all available atom types" />
+        </section>
+        <section name="misc" title="Misc">
+            <param argument="--seed" type="integer" optional="true" label="Explicit random seed" />
+            <param argument="--exhaustiveness" type="integer" value="8" label="Exhaustiveness of the global search" />
+            <param argument="--num_modes" type="integer" min="1" value="9" label="Maximum number of binding modes to generate" />
+            <param argument="--energy_range" type="float" value="3" label="Maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" />
+            <param argument="--min_rmsd_filter" type="float" value="1" label="Rmsd value used to filter final poses to remove redundancy" />
+            <param argument="--addH" type="boolean" truevalue="" falsevalue="--addH false" checked="true" label="Automatically add hydrogens in ligands" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="pdbqt" from_work_dir="ligand_out.pdbqt" />
+        <data name="out_flex_output" format="txt" label="smina: flexible receptor residues">
+            <filter>output_sect['out_flex']</filter>
+        </data>
+        <data name="output_log" format="txt" label="smina: log file">
+            <filter>output_sect['log']</filter>
+        </data>
+        <data name="atom_terms_output" format="txt" label="smima: per-atom interaction term values">
+            <filter>output_sect['atom_terms']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="receptor" value="protein.pdbqt" />
+            <param name="ligand" value="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" />
+            <param name="log" value="True" />
+            <param name="seed" value="1000" />
+            <param name="num_modes" value="5" />
+            <output name="output" file="ligand_out.pdbqt" />
+            <output name="output_log" file="output_smina" />
+        </test>
+    </tests>
+    <help><![CDATA[
+************
+Description
+************
+
+`smina <https://sourceforge.net/projects/smina/>`_ is a fork of `AutoDock Vina <http://vina.scripps.edu/>`_ that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/ci300604z</citation>
+    </citations>
+</tool>