annotate antechamber.xml @ 0:c01897428864 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
author chemteam
date Thu, 13 Jun 2019 03:52:54 -0400
parents
children 59a0424937cc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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1 <tool id="ambertools_antechamber" name="AnteChamber" version="@VERSION@">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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2 <description>Amber's molecular input file processor</description>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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3 <macros>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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4 <import>macros.xml</import>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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5 </macros>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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6 <expand macro="requirements"></expand>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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7 <command detect_errors="exit_code">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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8 <![CDATA[
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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9 antechamber -i '$input1'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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10 -o '$output1'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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11 -fi '$input1.ext'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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12 -fo '$selected_output_format'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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13 -c '$allparams.c'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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14 -pf '$extraparams.pf'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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15 #if '$extraparams.usenc'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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16 -nc '$allparams.nc'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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17 #end if
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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18 -at '$allparams.at'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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19 -j '$allparams.j'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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20 -rn '$allparams.resname'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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21 -m '$allparams.m'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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22 ]]>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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23 </command>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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24 <inputs>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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25 <param type="data" name="input1" label="Molecular input (PDB or mol2)" format="pdb,mol2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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26 <param name="selected_output_format" type="select" label="Select an output file format (mol2 recommended!):">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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27 <option value="pdb">pdb</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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28 <option value="mol2" selected="true">mol2</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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29 </param>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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30 <section name="allparams" title="General Parameters" expanded="true">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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31 <param name="nc" type="integer" value="0" label="Net charge" min="-50" max="50" help="Specify the net charge for the molecule. Default is 0. (-nc)"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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32 <param name="m" type="integer" value="1" label="Multiplicity" min="1" max="10" help="Multiplicity, 2S+1. Default is 1. (-m)"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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33 <param name="resname" type="text" value="MOL" label="Residue name" help="From 1-3 characters allowed. Default is MOL. (-rn)"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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34 <param name="c" type="select" label="Charge method" help="Charge method to use for the calculations. AM1-BCC or RESP recommended (-c)">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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35 <option value="resp">RESP</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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36 <option selected="True" value="bcc">AM1-BCC</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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37 <option value="cm1">CM1</option>
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38 <option value="cm2">CM2</option>
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39 <option value="esp">ESP (Kollman)</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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40 <option value="mul">Mulliken</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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41 <option value="gas">Gasteiger</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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42 </param>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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43 <param name="at" type="select" label="Atom type" help="Create atom type for the specified forcefield (-at)">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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44 <option selected="True" value="gaff">gaff</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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45 <option value="gaff2">gaff2</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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46 <option value="amber">amber for PARM94/99/99SB</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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47 <option value="bcc">bcc</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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48 <option value="sybyl">sybyl</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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49 </param>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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50 <param name="j" type="select" label="Atom type and bond type prediction index" help="Specify how to run predictions (-j)">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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51 <option value="0">0 - No assignment</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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52 <option value="1">1 - atom type</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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53 <option value="2">2 - full bond types</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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54 <option value="3">3 - part bond types</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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55 <option selected="True" value="4">4 - atom and full bond type (default)</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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56 <option value="5">5 - atom and part bond type</option>
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57 </param>
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58 </section>
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59 <section name="extraparams" title="Additional Parameters" expanded="false">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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60 <param name="pf" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="remove intermediate files (recommended)" help="(-pf)"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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61 <param name="usenc" type="boolean" checked="true" truevalue="True" falsevalue="False" label="use netcharge (recommended)" help="Can choose to let the charge be inferred by setting this to False."/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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62 </section>
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63 </inputs>
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64 <outputs>
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65 <data format="mol2" name="output1" label="${tool.name}: structure output">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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66 <change_format>
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67 <when input="selected_output_format" value="pdb" format="pdb"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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68 <when input="selected_output_format" value="mol2" format="mol2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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69 <!-- <when input="selected_format" value="xyz" format="xyz"/> <when input="selected_format" value="tinker" format="tinker"/> <when input="selected_format" value="moldy" format="moldy"/> -->
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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70 </change_format>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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71 </data>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="input1" value="LigA.mol2"/>
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76 <section name="allparams">
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77 <param name="nc" value="-2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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78 <param name="c" value="AM1-BCC"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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79 <param name="at" value="gaff2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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80 <param name="j" value="5 - atom and part bond type"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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81 </section>
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82 <output name="output1" file="LigA_output.mol2" compare="diff" lines_diff="0">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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83 <assert_contents>
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84 <has_text text=" 1 C 49.2110 26.9920 85.5530 c2 1 MOL"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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85 </assert_contents>
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86 </output>
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87 </test>
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88 <test>
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89 <param name="input1" value="LigA.pdb" ftype="pdb"/>
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90 <param name="selected_output_format" value="pdb"/>
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91 <section name="allparams">
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92 <param name="nc" value="-2"/>
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93 <param name="c" value="AM1-BCC"/>
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94 <param name="at" value="gaff2"/>
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95 <param name="j" value="5 - atom and part bond type"/>
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96 </section>
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97 <output name="output1" file="LigA_output.pdb" compare="diff" lines_diff="0">
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98 <assert_contents>
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99 <has_text text="ATOM 1 C MOL 1 49.211 26.992 85.553 1.00 0.00 C"/>
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100 </assert_contents>
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101 </output>
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102 </test>
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103 </tests>
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104 <help>
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105 <![CDATA[
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106 .. class:: infomark
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107
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108 **What it does**
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109
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110 Antechamber sets up parameters for the input molecules provided.
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111
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112 .. class:: infomark
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113
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114 **How it works**
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115
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116 - Select an input file (PDB, mol2)
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117 - Specify the correct charge, or keep the default charge of 0
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118 - Adjust other parameters as needed.
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119 - Click on Execute
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120
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121 .. class:: infomark
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122
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123 **Outputs created**
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124
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125 - A mol2 or PDB output is created with the forcefield compatible atom names.
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126
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127 .. class:: infomark
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128
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129 **User guide and documentation**
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130
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131 - AmberTools `userguide`_
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132
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133
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134 .. _`userguide`: http://ambermd.org/doc12/Amber19.pdf
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135
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136 .. class:: infomark
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137
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138 **Feature requests**
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139
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140 Go to Galaxy Computational Chemistry and make a `feature request`_
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141
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142 .. _`feature request`: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/new
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143
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144
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145 ]]>
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146 </help>
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147 <expand macro="citations"/>
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148 </tool>