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annotate parmchk2.xml @ 0:a1a204464657 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
author chemteam
date Thu, 13 Jun 2019 03:52:29 -0400
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a1a204464657 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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1 <tool id="ambertools_parmchk2" name="ParmChk2" version="@VERSION@">
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2 <description>Amber's parameter checker</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"></expand>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 parmchk2 -i '$input1'
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10 -f '$input1.ext'
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11 -s '$allparams.s'
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12 -a '$allparams.a'
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13 -o '$output1'
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param type="data" name="input1" label="Molecular input (mol2)" format="mol2"/>
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18 <section name="allparams" title="General Parameters" expanded="true">
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19 <param name="s" type="select" display="radio" label="FFparm set parameter" help="(-s)">
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20 <option selected="True" value="1">1: gaff</option>
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21 <option value="2">2: gaff2</option>
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22 </param>
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23 <param name="a" type="boolean" checked="false" truevalue="Y" falsevalue="N" label="Print all force field parameters" help="(-a)"/>
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24 </section>
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25 </inputs>
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26 <outputs>
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27 <data format="txt" name="output1" label="${tool.name}: frcmod output"></data>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input1" value="LigA_prmchk.mol2"/>
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32 <section name="allparams">
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33 <param name="s" value="2"/>
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34 </section>
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35 <output name="output1" file="LigA_output.txt" compare="diff" lines_diff="0"></output>
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36 </test>
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37 </tests>
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38 <help>
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39 <![CDATA[
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40 .. class:: infomark
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41
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42 **What it does**
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43
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44 Antechamber parameter check reads in a mol2 file and writes out a force field modification (frcmod) file containing any force field parameters that are needed for the molecule but not supplied by the force field file.
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45 Problematic parameters, if any, are indicated in the frcmod file with the note, “ATTN, need revision”, and are typically given values of zero.
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46
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47
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48 .. class:: infomark
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49
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50 **How it works**
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51
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52 - Select a mol input file (mol2)
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53 - Choose GAFF or GAFF2 parameter set
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54
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55 .. class:: infomark
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56
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57 **Outputs created**
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59 - Outputs a frcmod file as text
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61 .. class:: infomark
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62
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63 **User guide and documentation**
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64
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65 - AmberTools `userguide`_
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66
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68 .. _`userguide`: http://ambermd.org/doc12/Amber19.pdf
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69
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70 .. class:: infomark
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72 **Feature requests**
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73
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74 Go to Galaxy Computational Chemistry and make a `feature request`_
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76 .. _`feature request`: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/new
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77
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78 ]]>
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79 </help>
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80 <expand macro="citations"/>
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81 </tool>