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annotate biobb_fix_side_chain.xml @ 2:4c626e984fde draft default tip

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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_fix_side_chain" name="Fix Side Chain" version="0.1.5" >
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2 <description>: reconstructs the missing side chains and heavy atoms.</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 #if $config.sele == "option1":
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9 ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
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10 #end if
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11 docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_model:0.1.5--py_0 fix_side_chain --input_pdb_path $inputname.${inputname.ext}
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12 #if $config.sele == "option1":
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13 --config ${config.properties}.${config.properties.ext}
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14 #else if $config.sele == "option2":
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15 --config ${config.jsonstr}
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16 #end if
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17 --output_pdb_path $output;
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18 #if $config.sele == "option1":
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19 rm -f ${config.properties}.${config.properties.ext};
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20 #end if
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21 rm -f ${inputname}.${inputname.ext}
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22 </command>
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23 <inputs>
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24 <param name="outname" type="text" value="myFixSideChain.pdb" label="Output PDB name" help="Name for the Output list. Format: [output].pdb "/>
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25 <param name="inputname" type="data" format="pdb" label="Input PDB file" help="Select your input PDB file. Format: [input].pdb"/>
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26 <conditional name="config">
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27 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
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28 <option value="option1">from configuration file</option>
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29 <option value="option2">from JSON string</option>
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30 <option value="option3" selected="true">by default</option>
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31 </param>
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32 <when value="option1">
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33 <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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34 </when>
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35 <when value="option2">
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36 <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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37 </when>
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38 <when value="option3">
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39 </when>
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40
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41 </conditional>
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42 </inputs>
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43 <outputs>
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44 <data name="output" format="pdb" label="${outname}"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="inputname" value="../test-data/2ki5.pdb"/>
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49 <output name="output" file="../test-data/biobb_fix_side_chain_myFixSideChain.pdb"/>
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50 </test>
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51 </tests>
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52 <help>
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53 .. class:: warningmark
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54
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55
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56 Check the syntax for setting the tool parameters at the original library documentation: https://biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_side_chain
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57
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58 -----
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59
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60 .. image:: ${static_path}/images/biobb.png
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61 :height: 57
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62 :width: 150
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63
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64
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65 **https://bioexcel.eu**
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66 </help>
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67 <citations>
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68 <citation type="bibtex">
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69 @misc{githubbiobb,
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70 author = {Andrio P, Hospital A, Gelpi JL},
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71 year = {2019},
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72 title = {biobb: BioExcel building blocks },
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73 publisher = {GitHub},
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74 journal = {GitHub repository},
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75 url = {https://github.com/bioexcel/biobb_io},
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76 }</citation>
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77 </citations>
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78 </tool>