Mercurial > repos > earlhaminst > smina

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

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
author earlhaminst
date Tue, 08 May 2018 19:08:15 -0400
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7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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diff changeset
1 <tool id="smina" name="smina" version="1.0">
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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2 <description>Scoring and Minimization with AutoDock Vina</description>
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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3 <requirements>
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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4 <requirement type="package" version="2017.11.9">smina</requirement>
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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5 </requirements>
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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6 <command detect_errors="exit_code"><![CDATA[
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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7 ln -s '$input.receptor' receptor.pdbqt &&
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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8 ln -s '$input.ligand' ligand.pdbqt &&
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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9 smina
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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10 --receptor receptor.pdbqt
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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11 --ligand ligand.pdbqt
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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12 #if $input.flex
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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13 --flex '$input.flex'
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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14 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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15 #if $input.flexres
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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16 --flexres '$input.flexres'
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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17 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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18 #if $input.flexdist_ligand
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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19 --flexdist_ligand '$input.flexdist_ligand'
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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20 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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21 #if str($input.flexdist)
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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22 --flexdist $input.flexdist
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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23 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
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24
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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25 --center_x $search_space.center_x
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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26 --center_y $search_space.center_y
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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27 --center_z $search_space.center_z
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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28 --size_x $search_space.size_x
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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29 --size_y $search_space.size_y
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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30 --size_z $search_space.size_z
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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31 #if $search_space.autobox_ligand
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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32 --autobox_ligand '$search_space.autobox_ligand'
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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33 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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34 #if str($search_space.autobox_add)
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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35 --autobox_add $search_space.autobox_add
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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36 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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37 $search_space.no_lig
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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38
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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39 --out ligand_out.pdbqt
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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40 #if $output_sect.out_flex
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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41 --out_flex '$out_flex_output'
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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42 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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43 #if $output_sect.log
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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44 --log '$output_log'
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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45 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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46 #if $output_sect.atom_terms
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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47 --atom_terms '$atom_terms_output'
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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48 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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49 $output_sect.atom_term_data
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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50
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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51 --scoring $scoring_and_minimization.scoring
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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52 #if $scoring_and_minimization.custom_scoring
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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53 --custom_scoring '$scoring_and_minimization.custom_scoring'
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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54 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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55 #if $scoring_and_minimization.custom_atoms
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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56 --custom_atoms '$scoring_and_minimization.custom_atoms'
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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57 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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58 $scoring_and_minimization.score_only
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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59 $scoring_and_minimization.local_only
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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60 $scoring_and_minimization.minimize
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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61 $scoring_and_minimization.randomize_only
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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62 --minimize_iters $scoring_and_minimization.minimize_iters
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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63 $scoring_and_minimization.accurate_line
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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64 $scoring_and_minimization.minimize_early_term
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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65 #if $scoring_and_minimization.approximation
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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66 --approximation $scoring_and_minimization.approximation
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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67 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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68 #if $scoring_and_minimization.factor
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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69 --factor $scoring_and_minimization.factor
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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70 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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71 #if str($scoring_and_minimization.force_cap)
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
parents:
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72 --force_cap $scoring_and_minimization.force_cap
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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73 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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74 #if str($scoring_and_minimization.user_grid)
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
parents:
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75 --user_grid $scoring_and_minimization.user_grid
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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76 #end if
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
parents:
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77 --user_grid_lambda $scoring_and_minimization.user_grid_lambda
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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78 $scoring_and_minimization.print_terms
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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79 $scoring_and_minimization.print_atom_types
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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80
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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81 --cpu \${GALAXY_SLOTS:-1}
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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82 #if str($misc.seed)
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
earlhaminst
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83 --seed $misc.seed
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84 #end if
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85 --exhaustiveness $misc.exhaustiveness
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86 --num_modes $misc.num_modes
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87 --energy_range $misc.energy_range
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88 --min_rmsd_filter $misc.min_rmsd_filter
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89 $misc.addH
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90 ]]></command>
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91 <inputs>
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92 <section name="input" title="Input" expanded="True">
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93 <param argument="--receptor" type="data" format="pdbqt" label="Rigid part of the receptore" />
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94 <param argument="--ligand" type="data" format="pdbqt" label="Ligand(s)" />
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95 <param argument="--flex" type="data" format="pdbqt" optional="true" label="Flexible side chains, if any" />
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96 <param argument="--flexres" type="text" optional="true" label="Flexible side chains specified by comma separated list of chain:resid" />
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97 <param argument="--flexdist_ligand" type="data" format="data" optional="true" label="Ligand to use for flexdist" />
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98 <param argument="--flexdist" type="float" optional="true" label="Set all side chains within specified distance to flexdist_ligand to flexible" />
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99 </section>
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100 <section name="search_space" title="Search space" expanded="True">
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101 <param argument="--center_x" type="float" value="0" label="X coordinate of the center" />
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102 <param argument="--center_y" type="float" value="0" label="Y coordinate of the center" />
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103 <param argument="--center_z" type="float" value="0" label="Z coordinate of the center" />
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104 <param argument="--size_x" type="integer" value="1" label="Size in the X dimension" />
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105 <param argument="--size_y" type="integer" value="1" label="Size in the Y dimension" />
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106 <param argument="--size_z" type="integer" value="1" label="Size in the Z dimension" />
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107
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108 <param argument="--autobox_ligand" type="data" format="data" optional="true" label="Ligand to use for autobox" />
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109 <param argument="--autobox_add" type="float" optional="true" label="Amount of buffer space to add to auto-generated box text" />
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110 <param argument="--no_lig" type="boolean" truevalue="--no_lig" falsevalue="" label="No ligand; for sampling/minimizing flexible residues" />
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111 </section>
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112 <section name="output_sect" title="Output">
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113 <param argument="--out_flex" type="boolean" label="Write flexible receptor residues" />
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114 <param argument="--log" type="boolean" label="Write log file" />
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115 <param argument="--atom_terms" type="boolean" label="Write per-atom interaction term values" />
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116 <param argument="--atom_term_data" type="boolean" truevalue="--atom_term_data" falsevalue="" label="Embedded per-atom interaction terms in output sd data" />
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117 </section>
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118 <section name="scoring_and_minimization" title="Scoring and minimization options">
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119 <param argument="--scoring" type="select" label="Specify alternative builtin scoring function">
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120 <option value="default" selected="true">default</option>
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121 <option value="ad4_scoring">ad4_scoring</option>
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122 <option value="dkoes_fast">dkoes_fast</option>
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123 <option value="dkoes_scoring">dkoes_scoring</option>
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124 <option value="dkoes_scoring_old">dkoes_scoring_old</option>
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125 <option value="vina">vina</option>
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126 <option value="vinardo">vinardo</option>
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127 </param>
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128 <param argument="--custom_scoring" type="data" format="data" optional="true" label="Custom scoring function file" />
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129 <param argument="--custom_atoms" type="data" format="data" optional="true" label="Custom atom type parameters file" />
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130 <param argument="--score_only" type="boolean" truevalue="--score_only" falsevalue="" label="Score provided ligand pose" />
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131 <param argument="--local_only" type="boolean" truevalue="--local_only" falsevalue="" label="Local search only using autobox" />
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132 <param argument="--minimize" type="boolean" truevalue="--minimize" falsevalue="" label="Energy minimization" />
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133 <param argument="--randomize_only" type="boolean" truevalue="--randomize_only" falsevalue="" label="Generate random poses, attempting to avoid clashes" />
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134 <param argument="--minimize_iters" type="integer" value="0" label="Number iterations of steepest descent" />
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135 <param argument="--accurate_line" type="boolean" truevalue="--accurate_line" falsevalue="" label="Accurate line search" />
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136 <param argument="--minimize_early_term" type="boolean" truevalue="--minimize_early_term" falsevalue="" label="Stop minimization before convergence conditions are fully met" />
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137 <param argument="--approximation" type="select" optional="true" label="Approximation">
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138 <option value="linear">linear</option>
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139 <option value="spline">spline</option>
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140 <option value="exact">exact</option>
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141 </param>
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142 <param argument="--factor" type="float" min="0" optional="true" label="Approximation factor: higher results in a finer-grained approximation" />
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143 <param argument="--force_cap" type="float" optional="true" label="Max allowed force; lower values more gently minimize clashing structures" />
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144 <param argument="--user_grid" type="float" optional="true" label="Autodock map file for user grid data based calculations" />
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145 <param argument="--user_grid_lambda" type="float" value="-1" label="Scales user_grid and functional scoring" />
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146 <param argument="--print_terms" type="boolean" truevalue="--print_terms" falsevalue="" label="Print all available terms with default parameterizations" />
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147 <param argument="--print_atom_types" type="boolean" truevalue="--print_atom_types" falsevalue="" label="Print all available atom types" />
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148 </section>
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149 <section name="misc" title="Misc">
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150 <param argument="--seed" type="integer" optional="true" label="Explicit random seed" />
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151 <param argument="--exhaustiveness" type="integer" value="8" label="Exhaustiveness of the global search" />
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152 <param argument="--num_modes" type="integer" min="1" value="9" label="Maximum number of binding modes to generate" />
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153 <param argument="--energy_range" type="float" value="3" label="Maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" />
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154 <param argument="--min_rmsd_filter" type="float" value="1" label="Rmsd value used to filter final poses to remove redundancy" />
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155 <param argument="--addH" type="boolean" truevalue="" falsevalue="--addH false" checked="true" label="Automatically add hydrogens in ligands" />
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156 </section>
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157 </inputs>
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158 <outputs>
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159 <data name="output" format="pdbqt" from_work_dir="ligand_out.pdbqt" />
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160 <data name="out_flex_output" format="txt" label="smina: flexible receptor residues">
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161 <filter>output_sect['out_flex']</filter>
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162 </data>
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163 <data name="output_log" format="txt" label="smina: log file">
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164 <filter>output_sect['log']</filter>
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165 </data>
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166 <data name="atom_terms_output" format="txt" label="smima: per-atom interaction term values">
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
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167 <filter>output_sect['atom_terms']</filter>
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168 </data>
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169 </outputs>
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170 <tests>
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171 <test>
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172 <param name="receptor" value="protein.pdbqt" />
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
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173 <param name="ligand" value="ligand.pdbqt" />
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174 <param name="center_x" value="11" />
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175 <param name="center_y" value="90.5" />
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176 <param name="center_z" value="57.5" />
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177 <param name="size_x" value="22" />
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178 <param name="size_y" value="24" />
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179 <param name="size_z" value="28" />
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180 <param name="log" value="True" />
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181 <param name="seed" value="1000" />
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182 <param name="num_modes" value="5" />
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183 <output name="output" file="ligand_out.pdbqt" />
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184 <output name="output_log" file="output_smina" />
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185 </test>
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186 </tests>
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187 <help><![CDATA[
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
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188 ************
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189 Description
7c0bb0c48a27 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
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190 ************
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191
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192 `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.
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193 ]]></help>
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194 <citations>
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195 <citation type="doi">10.1021/ci300604z</citation>
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196 </citations>
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197 </tool>