Mercurial > repos > chemteam > ambertools_parmchk2
annotate parmchk2.xml @ 2:00ff41b1d49a draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:45:54 -0400 |
| parents | a1a204464657 |
| children | 6aa2b60f3195 |
| rev | line source |
|---|---|
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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changeset
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1 <tool id="ambertools_parmchk2" name="ParmChk2" version="@VERSION@"> |
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2
00ff41b1d49a
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
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2 <description>- Amber's parameter checker</description> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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3 <macros> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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4 <import>macros.xml</import> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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changeset
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5 </macros> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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changeset
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6 <expand macro="requirements"></expand> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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changeset
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7 <command detect_errors="exit_code"> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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8 <![CDATA[ |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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9 parmchk2 -i '$input1' |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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10 -f '$input1.ext' |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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11 -s '$allparams.s' |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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12 -a '$allparams.a' |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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13 -o '$output1' |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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14 ]]> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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15 </command> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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16 <inputs> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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17 <param type="data" name="input1" label="Molecular input (mol2)" format="mol2"/> |
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2
00ff41b1d49a
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
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18 <section name="allparams" title="General parameters" expanded="true"> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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19 <param name="s" type="select" display="radio" label="FFparm set parameter" help="(-s)"> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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20 <option selected="True" value="1">1: gaff</option> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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21 <option value="2">2: gaff2</option> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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22 </param> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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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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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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24 </section> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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changeset
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25 </inputs> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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changeset
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26 <outputs> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff
changeset
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27 <data format="txt" name="output1" label="${tool.name}: frcmod output"></data> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff
changeset
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28 </outputs> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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29 <tests> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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30 <test> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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31 <param name="input1" value="LigA_prmchk.mol2"/> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff
changeset
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32 <section name="allparams"> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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33 <param name="s" value="2"/> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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34 </section> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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35 <output name="output1" file="LigA_output.txt" compare="diff" lines_diff="0"></output> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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36 </test> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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37 </tests> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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changeset
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38 <help> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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39 <![CDATA[ |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
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40 .. class:: infomark |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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41 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
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42 **What it does** |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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43 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
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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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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
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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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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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46 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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47 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
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48 .. class:: infomark |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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49 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
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50 **How it works** |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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51 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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52 - Select a mol input file (mol2) |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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53 - Choose GAFF or GAFF2 parameter set |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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54 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
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55 .. class:: infomark |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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56 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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57 **Outputs created** |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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58 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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59 - Outputs a frcmod file as text |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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60 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
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61 .. class:: infomark |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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62 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
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63 **User guide and documentation** |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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64 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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65 - AmberTools `userguide`_ |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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66 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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67 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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68 .. _`userguide`: http://ambermd.org/doc12/Amber19.pdf |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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69 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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70 .. class:: infomark |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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71 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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72 **Feature requests** |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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73 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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74 Go to Galaxy Computational Chemistry and make a `feature request`_ |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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75 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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76 .. _`feature request`: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/new |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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77 |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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78 ]]> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
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79 </help> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
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80 <expand macro="citations"/> |
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a1a204464657
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
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81 </tool> |