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biobb_genion.xml
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biobb_genion.xml
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<tool id="biobb_genion" name="Genion" version="0.1.5">
<description>: adding ions to Gromacs topology</description>
<requirements>
<requirement type="binary">docker</requirement>
</requirements>
<command detect_errors="aggressive">
ln -f -s ${inputname} ${inputname}.${inputname.ext};
ln -f -s ${inputzip} ${inputzip}.${inputzip.ext};
#if $config.sele == "option1":
ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
#end if
docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 genion --input_tpr_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext}
#if $config.sele == "option1":
--config ${config.properties}.${config.properties.ext}
#else if $config.sele == "option2":
--config ${config.jsonstr}
#end if
--output_gro_path $__root_dir__/database/files/000/$outname
--output_top_zip_path $outputzip;
#if $config.sele == "option1":
rm -f ${config.properties}.${config.properties.ext};
#end if
rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext};
mv $__root_dir__/database/files/000/$outname $output
</command>
<inputs>
<param name="outname" type="text" value="myGenion.gro" label="Output GRO name" help="Name for the Output. Format: [output].gro "/>
<param name="outnamezip" type="text" value="myGenion.zip" label="Output ZIP name" help="Name for the Output topology TOP and ITP files. Format: [output].zip "/>
<param name="inputname" type="data" format="tpr" label="Input TPR file" help="Select your input portable run TPR file. Format: [input].tpr"/>
<param name="inputzip" type="data" format="zip" label="Input ZIP file" help="Select your input topology TOP and ITP files zipball. Format: [input].zip"/>
<conditional name="config">
<param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
<option value="option1">from configuration file</option>
<option value="option2">from JSON string</option>
<option value="option3" selected="true">by default</option>
</param>
<when value="option1">
<param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
</when>
<when value="option2">
<param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
</when>
<when value="option3">
</when>
</conditional>
</inputs>
<outputs>
<data name="output" format="gro" label="${outname}"/>
<data name="outputzip" format="zip" label="${outnamezip}"/>
</outputs>
<tests>
<test>
</test>
</tests>
<help>
.. class:: warningmark
Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.genion
-----
The main output of this BB will be an updated post-procesed Gromacs structure file (.gro) and a zip file containing the updated topology file (.top) and the restriction files (.itp).
.. image:: ${static_path}/images/biobb.png
:height: 57
:width: 150
**https://bioexcel.eu**
</help>
<citations>
<citation type="bibtex">
@misc{githubbiobb,
author = {Andrio P, Hospital A, Gelpi JL},
year = {2019},
title = {biobb: BioExcel building blocks },
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/bioexcel/biobb_io},
}</citation>
</citations>
</tool>