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author spanish_national_institue_of_bioinformatics
date Fri, 12 Apr 2019 07:18:48 -0400
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1 <tool id="biobb_grompp" name="Grompp" version="0.1.5" >
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2 <description>:Gromacs preprocessor. Reads topology file to create TPR atomic description</description>
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3 <requirements>
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4 <requirement type="binary">docker</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive">
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7 ln -f -s ${inputname} ${inputname}.${inputname.ext};
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8 ln -f -s ${inputzip} ${inputzip}.${inputzip.ext};
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9 ln -f -s ${inputgro} ${inputgro}.${inputgro.ext};
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10 #if $config.sele == "option1":
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11 ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
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12 #end if
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13 docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 grompp --input_cpt_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} --input_gro_path ${inputgro}.${inputgro.ext}
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14 #if $config.sele == "option1":
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15 --config ${config.properties}.${config.properties.ext}
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16 #else if $config.sele == "option2":
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17 --config ${config.jsonstr}
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18 #end if
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19 --output_tpr_path $__root_dir__/database/files/000/$outname;
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20 #if $config.sele == "option1":
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21 rm -f ${config.properties}.${config.properties.ext};
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22 #end if
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23 rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext} ${inputgro}.${inputgro.ext};
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24 mv $__root_dir__/database/files/000/$outname $output_tpr
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25 </command>
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26 <inputs>
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27 <param name="inputgro" type="data" format="gro" label="Structure file" help="Select your input GROMACS structure file. Format: [input].gro"/>
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28 <param name="inputzip" type="data" format="zip" label="Topology file" help="Select your input GROMACS topology TOP and ITP file. Format: [input].zip"/>
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29 <param name="inputname" type="data" format="cpt" label="Check point file" optional="True" help="Select your input GROMACS checkpoint file. Format: [input].cpt"/>
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30 <param name="outname" type="text" value="myGrompp.tpr" label="Output TPR name" help="Name for the Output binary run file. Format: [output].tpr "/>
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31 <conditional name="config">
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32 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
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33 <option value="option1">from configuration file</option>
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34 <option value="option2">from JSON string</option>
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35 <option value="option3" selected="true">by default</option>
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36 </param>
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37 <when value="option1">
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38 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
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39 </when>
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40 <when value="option2">
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41 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
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42 </when>
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43 <when value="option3">
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44 </when>
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45 </conditional>
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46 </inputs>
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47 <outputs>
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48 <data name="output_tpr" format="tpr" label="${outname}"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 </test>
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53 </tests>
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54 <help>
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55 .. class:: warningmark
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56
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57
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58 Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp
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59
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60 -----
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61
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62 .. image:: ${static_path}/images/biobb.png
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63 :height: 57
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64 :width: 150
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65
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66
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67 **https://bioexcel.eu**
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68 </help>
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69 <citations>
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70 <citation type="bibtex">
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71 @misc{githubbiobb,
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72 author = {Andrio P, Hospital A, Gelpi JL},
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73 year = {2019},
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74 title = {biobb: BioExcel building blocks },
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75 publisher = {GitHub},
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76 journal = {GitHub repository},
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77 url = {https://github.com/bioexcel/biobb_io},
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78 }</citation>
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79 </citations>
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80 </tool>