biobb: biobb_genrestr.xml annotate

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

Uploaded

author	spanish_national_institue_of_bioinformatics
date	Fri, 12 Apr 2019 07:18:48 -0400
parents
children

rev	line source
2 4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	1 <tool id="biobb_genrestr" name="Genrestr" version="0.1.5" >
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	2 <description>: creates a new zip Gromacs topology applying the indicated force restrains</description>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	3 <requirements>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	4 <requirement type="binary">docker</requirement>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	5 </requirements>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	6 <command detect_errors="aggressive">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	7 ln -f -s ${inputname} ${inputname}.${inputname.ext};
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	8 ln -f -s ${inputzip} ${inputzip}.${inputzip.ext};
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	9 ln -f -s ${inputstr} ${inputstr}.${inputstr.ext};
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	10 #if $config.sele == "option1":
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	11 ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	12 #end if
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	13 docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 genrestr --input_ndx_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} --input_structure_path ${inputstr}.${inputstr.ext}
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	14 #if $config.sele == "option1":
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	15 --config ${config.properties}.${config.properties.ext}
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	16 #else if $config.sele == "option2":
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	17 --config ${config.jsonstr}
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	18 #end if
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	19 --output_top_zip_path $outputzip;
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	20 #if $config.sele == "option1":
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	21 rm -f ${config.properties}.${config.properties.ext};
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	22 #end if
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	23 rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext} ${inputstr}.${inputstr.ext}
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	24 </command>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	25 <inputs>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	26 <param name="outnamezip" type="text" value="myGenrestr.zip" label="Output ZIP name" help="Name for the Output TOP topology. Format: [output].zip "/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	27 <param name="inputstr" type="data" format="pdb,gro,tpr" label="Structure file" help="Select your input structure. Format: [input].pdb or [input].gro or [input].tpr"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	28 <param name="inputname" type="data" format="ndx" label="Index file" help="Select your input GROMACS index file. Format: [input].ndx"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	29 <param name="inputzip" type="data" format="zip" label="ZIP file" help="Select your input ZIP file. Format: [input].zip"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	30 <conditional name="config">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	31 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	32 <option value="option1">from configuration file</option>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	33 <option value="option2">from JSON string</option>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	34 <option value="option3" selected="true">by default</option>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	35 </param>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	36 <when value="option1">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	37 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	38 </when>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	39 <when value="option2">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	40 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	41 </when>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	42 <when value="option3">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	43 </when>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	44 </conditional>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	45 </inputs>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	46 <outputs>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	47 <data name="outputzip" format="zip" label="${outnamezip}"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	48 </outputs>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	49 <tests>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	50 <test>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	51 </test>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	52 </tests>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	53 <help>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	54 .. class:: warningmark
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	55
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	56
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	57 Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.genrestr
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	58
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	59 -----
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	60
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	61 .. image:: ${static_path}/images/biobb.png
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	62 :height: 57
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	63 :width: 150
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	64
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	65
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	66 https://bioexcel.eu
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	67 </help>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	68 <citations>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	69 <citation type="bibtex">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	70 @misc{githubbiobb,
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	71 author = {Andrio P, Hospital A, Gelpi JL},
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	72 year = {2019},
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	73 title = {biobb: BioExcel building blocks },
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	74 publisher = {GitHub},
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	75 journal = {GitHub repository},
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	76 url = {https://github.com/bioexcel/biobb_io},
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	77 }</citation>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	78 </citations>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	79 </tool>

Mercurial > repos > spanish_national_institue_of_bioinformatics > biobb

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