Mercurial > repos > chemteam > acpype_amber2gromacs

annotate acpype_Amber2Gromacs.xml @ 0:79c856227ff1 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 10:00:44 +0000
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79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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1 <tool id="acpype_Amber2Gromacs" name="Convert Amber topology and coordinate files to GROMACS format" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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2 <description>using acpype</description>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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3 <macros>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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4 <import>macros.xml</import>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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5 <token name="@GALAXY_VERSION@">0</token>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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6 </macros>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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7 <expand macro="requirements">
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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8 <requirement type="package" version="2021.02.05.22.15">acpype</requirement>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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9 </expand>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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10 <command detect_errors="exit_code"><![CDATA[
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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11 ln -s '$input1' ./input1.${input1.ext} &&
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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12 ln -s '$input2' ./input2.${input2.ext} &&
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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13 acpype -p './input1.${input1.ext}' -x './input2.${input2.ext}'
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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14
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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15 ]]></command>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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16 <inputs>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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17 <param name="input1" type="data" format="txt" label="Amber Topology file" help="Topology file (prmtop) generated in Tleap"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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18 <param name="input2" type="data" format="txt" label="Amber Coordinate file" help="Coordinate file (inpcrd) generated in Tleap"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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19 </inputs>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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20 <outputs>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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21 <data format="top" name="top_output" label="GROMACS topology file" from_work_dir='*.top'/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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22 <data format="gro" name="gro_output" label="GROMACS coordinate file" from_work_dir="*.gro"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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23 </outputs>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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24 <tests>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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25 <test>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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26 <param name="input1" value="cid1.prmtop"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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27 <param name="input2" value="cid1.inpcrd"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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28 <output name="top_output">
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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29 <assert_contents>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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30 <has_line line="[ defaults ]"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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31 <has_text text="1 2 yes 0.5 0.8333"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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32 <has_text text=" ca ca 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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33 </assert_contents>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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34 </output>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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35 <output name="gro_output">
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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36 <assert_contents>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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37 <has_text text=" 42"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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38 <has_text text=" 1 UNL C1 1 41.372 -2.389 7.399"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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39 <has_text text=" 1 UNL H42 42 41.256 -2.276 7.041"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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40 <has_text text=" 11.59200 12.19000 23.64000"/>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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41 </assert_contents>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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42 </output>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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43 </test>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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44 </tests>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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45 <help><![CDATA[
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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46 Tool to produce GROMACS topology and coordinate files from systems generated with AmberTools' Tleap.
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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47
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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48 .. class:: infomark
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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49
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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50 **Input**
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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51
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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52 The input files are the standard topology (prmtop) and coordinate (inpcrd) files that are generally produced as outputs when processing a structure through Tleap.
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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53
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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54 .. class:: infomark
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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55
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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56 **Outputs**
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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57
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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58 GROMACS topology (TOP) and coordinate (GRO) files.
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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59
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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60 ]]></help>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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61 <expand macro="citations">
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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62 <citation type="doi">doi:10.1186/1756-0500-5-367</citation>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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63 </expand>
79c856227ff1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
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64 </tool>