Mercurial > repos > chemteam > ambertools_parmchk2

annotate parmchk2.xml @ 13:0c0104b3d5da draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
author chemteam
date Tue, 30 Nov 2021 09:59:22 +0000
parents 6aa2b60f3195
children
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6aa2b60f3195 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
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1 <tool id="ambertools_parmchk2" name="ParmChk2" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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00ff41b1d49a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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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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6aa2b60f3195 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <expand macro="requirements"></expand>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 parmchk2 -i '$input1'
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11 -f '$input1.ext'
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12 -s '$allparams.s'
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13 -a '$allparams.a'
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14 -o '$output1'
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param type="data" name="input1" label="Molecular input (mol2)" format="mol2"/>
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19 <section name="allparams" title="General parameters" expanded="true">
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20 <param name="s" type="select" display="radio" label="FFparm set parameter" help="(-s)">
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21 <option selected="True" value="1">1: gaff</option>
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22 <option value="2">2: gaff2</option>
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23 </param>
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24 <param name="a" type="boolean" checked="false" truevalue="Y" falsevalue="N" label="Print all force field parameters" help="(-a)"/>
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25 </section>
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26 </inputs>
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27 <outputs>
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28 <data format="txt" name="output1" label="${tool.name}: frcmod output"></data>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input1" value="LigA_prmchk.mol2"/>
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33 <section name="allparams">
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34 <param name="s" value="2"/>
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35 </section>
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36 <output name="output1" file="LigA_output.txt" compare="diff" lines_diff="0"></output>
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37 </test>
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38 </tests>
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39 <help>
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40 <![CDATA[
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41 .. class:: infomark
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43 **What it does**
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45 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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46 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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47
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49 .. class:: infomark
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50
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51 **How it works**
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53 - Select a mol input file (mol2)
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54 - Choose GAFF or GAFF2 parameter set
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56 .. class:: infomark
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58 **Outputs created**
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60 - Outputs a frcmod file as text
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62 .. class:: infomark
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64 **User guide and documentation**
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66 - AmberTools `userguide`_
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69 .. _`userguide`: http://ambermd.org/doc12/Amber19.pdf
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71 .. class:: infomark
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73 **Feature requests**
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75 Go to Galaxy Computational Chemistry and make a `feature request`_
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77 .. _`feature request`: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/new
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79 ]]>
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80 </help>
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81 <expand macro="citations"/>
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82 </tool>