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biobb_asitedesign.xml
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<tool id="biobb_asitedesign_asitedesign_ext" name="Asitedesign" version="1.0.0" >
<description>: Wrapper of the AsiteDesign module.</description>
<requirements>
<requirement type="package"
version="1.0.0"
>biobb_asitedesign</requirement>
</requirements>
<command detect_errors="aggressive"><![CDATA[
ln -f -s ${input_pdb} ${input_pdb}_`echo $$`.${input_pdb.ext};
ln -f -s ${input_yaml} ${input_yaml}_`echo $$`.${input_yaml.ext};
ln -f -s ${params_folder} ${params_folder}_`echo $$`.${params_folder.ext};
#if $config.sele == "option1":
ln -s -f ${config.properties} ${config.properties}_`echo $$`.${config.properties.ext};
#end if
asitedesign
#if $config.sele == "option1":
--config ${config.properties}.${config.properties.ext}
#else if $config.sele == "option2":
--config '${config.jsonstr}'
#else if $config.sele == "option3":
--config '__oc____dq__cpus__dq__:${properties.cpus},__dq__name__dq__:__dq__${properties.name}__dq__,__dq__DesignResidues__dq__:${properties.DesignResidues},__dq__CatalyticResidues__dq__:${properties.CatalyticResidues},__dq__Ligands__dq__:${properties.Ligands},__dq__Constraints__dq__:${properties.Constraints},__dq__nIterations__dq__:${properties.nIterations},__dq__nSteps__dq__:${properties.nSteps},__dq__nPoses__dq__:${properties.nPoses},__dq__Time__dq__:${properties.Time}__cc__'
#end if
#if str($input_pdb) != 'None':
--input_pdb ${input_pdb}_`echo $$`.${input_pdb.ext}
#end if
#if str($input_yaml) != 'None':
--input_yaml ${input_yaml}_`echo $$`.${input_yaml.ext}
#end if
#if str($params_folder) != 'None':
--params_folder ${params_folder}_`echo $$`.${params_folder.ext}
#end if
--output_path $outname_output_path
;
#if $config.sele == "option1":
rm -f ${config.properties}_`echo $$`.${config.properties.ext};
#end if
rm -f ${input_pdb}_`echo $$`.${input_pdb.ext};
rm -f ${input_yaml}_`echo $$`.${input_yaml.ext};
rm -f ${params_folder}_`echo $$`.${params_folder.ext};
if test -f $outname_output_path; then mv $outname_output_path $output_path; fi;
]]>
</command>
<inputs>
<param name="input_pdb" type="data" format="PDB" optional="False" label="input PDB file" help="Path to the input file pdb. Format: [input].PDB"/>
<param name="input_yaml" type="data" format="YAML" optional="False" label="input YAML file" help="Path to the input file yaml. Format: [input].YAML"/>
<param name="params_folder" type="data" format="PARAMS" optional="False" label="input PARAMS file" help="Path to the params folder. Format: [input].PARAMS"/>
<param name="outname_output_path" type="text" value="myasitedesign.zip"
optional="False" label="output ZIP name"
help="Path to the output file Format: [output].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="option3">Manual Input</option>
<option value="option1">from configuration file</option>
<option value="option2">from JSON string</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>
<section name="properties" title="Properties Input">
<param name="cpus" type="integer"
value="21"
label="cpus" help="Number of cpus for the job." optional="false"/>
<param name="name" type="text" label="name" help="Name of the job, which will be used for the output folders." optional="false"
value="DesignCatalyticSite_job"
>
<sanitizer><valid initial="string.printable"/></sanitizer>
</param>
<param name="DesignResidues" type="text" label="DesignResidues" help="List of residues that want to be mutable during the simulation. (Json)" value="[]" >
<sanitizer><valid initial="string.printable"/></sanitizer>
</param>
<param name="CatalyticResidues" type="text" label="CatalyticResidues" help="Specify the number of residues of the active site that wants to be added (RES1, RES2 ... RESN: H). (Json)" value="[]" >
<sanitizer><valid initial="string.printable"/></sanitizer>
</param>
<param name="Ligands" type="text" label="Ligands" help="1-L (you have to specify the ligand by giving the residue number and the chain of the specific LIG). Also, the torsions that want to be excluded must be specified by the user ("ExcludedTorsions"). (Json)" value="[]" >
<sanitizer><valid initial="string.printable"/></sanitizer>
</param>
<param name="Constraints" type="text" label="Constraints" help="Add the distance and sequence constraints that you want. The distance constraints should be added by passing two residues (with residue_number-chain) and two atoms (atomname) and to which values you want to constraint them (lb: value in angstroms, hb: value in angstroms). (Json)" value="[]" >
<sanitizer><valid initial="string.printable"/></sanitizer>
</param>
<param name="nIterations" type="integer"
value="20"
label="nIterations" help="Number of adaptive sampling epochs that want to be performed." optional="false"/>
<param name="nSteps" type="integer"
value="5"
label="nSteps" help="Number of steps performed in each epoch/iteration." optional="false"/>
<param name="nPoses" type="integer"
value="20"
label="nPoses" help="Number of final poses (mutants/designs) to be reported (each one given to a processor/CPU)." optional="false"/>
<param name="Time" type="integer"
value="48"
label="Time" help="Time in the queue (if it's run in a cluster)." optional="false"/>
</section>
</inputs>
<outputs>
<data name="output_path" format="zip" label="${outname_output_path}"/>
</outputs>
<tests>
<test>
</test>
</tests>
<help>
.. class:: infomark
Check the syntax for the tool parameters at the original library documentation: https://biobb_asitedesign.readthedocs.io/en/latest
-----
.. image:: http://mmb.irbbarcelona.org/biobb/assets/layouts/layout3/img/logo.png
:width: 150
**https://mmb.irbbarcelona.org/biobb**
.. image:: https://bioexcel.eu/wp-content/uploads/2019/08/Bioexcel_logo_no_subheading_660px.png
:width: 150
**https://bioexcel.eu**
</help>
<citations>
<citation type="bibtex">
@misc{githubbiobb,
author = {Andrio P, Bayarri, G., Hospital A, Gelpi JL},
year = {2019-21},
title = {biobb: BioExcel building blocks },
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/bioexcel/biobb_asitedesign},
}
</citation>
<citation type="doi">10.1038/s41597-019-0177-4</citation>
</citations>
</tool>