Mercurial > repos > spanish_national_institue_of_bioinformatics > biobb
diff biobb_pdb.xml @ 2:4c626e984fde draft default tip
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author | spanish_national_institue_of_bioinformatics |
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date | Fri, 12 Apr 2019 07:18:48 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobb_pdb.xml Fri Apr 12 07:18:48 2019 -0400 @@ -0,0 +1,72 @@ +<tool id="biobb_pdb" name="pdb" version="0.1.3" > + <description>: get PDB from rcsb.org</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command detect_errors="aggressive"> + #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_io:0.1.3--py_0 pdb + #if $config.sele == "option1": + --config ${config.properties}.${config.properties.ext} + #else if $config.sele == "option2": + --config ${config.jsonstr} + #end if + --output_pdb_path $output; + #if $config.sele == "option1": + rm -f ${config.properties}.${config.properties.ext}; + #end if + </command> + <inputs> + <param name="outname" type="text" value="myStructure.pdb" label="Output PDB name" help="Name for the Output list. Format: [output].pdb "/> + <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="pdb" label="${outname}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +.. class:: warningmark + + +Check the syntax for setting the tool parameters at the original library documentation: https://biobb-io.readthedocs.io/en/latest/mmb_api.html#module-mmb_api.pdb_variants + +----- + +.. 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>