biobb: biobb_mdrun.xml annotate

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_mdrun" name="Mdrun" version="0.1.5" >
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	2 <description>: performs molecular dynamics simulations from an input Gromacs TPR file. </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 #if $config.sele == "option1":
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	9 ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	10 #end if
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	11 docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 mdrun --input_tpr_path $inputname.${inputname.ext}
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	12 #if $config.sele == "option1":
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	13 --config ${config.properties}.${config.properties.ext}
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	14 #else if $config.sele == "option2":
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	15 --config ${config.jsonstr}
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	16 #end if
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	17 --output_log_path $__root_dir__/database/files/000/$outname_log
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	18 --output_gro_path $__root_dir__/database/files/000/$outname
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	19 --output_trr_path $__root_dir__/database/files/000/$outname_trr
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	20 --output_edr_path $__root_dir__/database/files/000//$outname_edr
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	21 --output_xtc_path $__root_dir__/database/files/000/$outname_xtc
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	22 --output_cpt_path $__root_dir__/database/files/000/$outname_cpt;
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	23 #if $config.sele == "option1":
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	24 rm -f ${config.properties}.${config.properties.ext};
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	25 #end if
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	26 rm -f ${inputname}.${inputname.ext};
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	27 mv $__root_dir__/database/files/000/$outname $output;
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	28 mv $__root_dir__/database/files/000/$outname_trr $output_trr;
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	29 mv $__root_dir__/database/files/000//$outname_edr $output_edr;
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	30 mv $__root_dir__/database/files/000/$outname_xtc $output_xtc;
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	31 mv $__root_dir__/database/files/000/$outname_cpt $output_cpt;
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	32 mv $__root_dir__/database/files/000/$outname_log $output_log
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	33 </command>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	34 <inputs>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	35 <param name="inputname" type="data" format="tpr" label="TPR file" help="Select your portable binary run input file. Format: [input].tpr"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	36 <param name="outname" type="text" value="mdrun.gro" label="Output GRO name" help="Name for the Output GROMACS structure. Format: [output].gro "/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	37 <param name="outname_trr" type="text" value="mdrun.trr" label="Output TRR name" help="Name for the Output GROMACS uncompressed raw. Format: [output].trr"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	38 <param name="outname_edr" type="text" value="mdrun.edr" label="Output EDR name" help="Name for the Output GROMACS portable energy file. Format: [output].edr"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	39 <param name="outname_xtc" type="text" value="mdrun.xtc" optional="True" label="Output XTC name" help="Name for the Output GROMACS compressed trajectory file. Format: [output].xtc"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	40 <param name="outname_cpt" type="text" value="mdrun.cpt" optional="True" label="Output CPT name" help="Name for the Output GROMACS checkpoint file. Format: [output].cpt"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	41 <param name="outname_log" type="text" value="mdrun.log" label="Output LOG name" help="Name for the Output GROMACS trajectory file. Format: [output].log"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	42 <conditional name="config">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	43 <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	44 <option value="option1">from configuration file</option>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	45 <option value="option2">from JSON string</option>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	46 <option value="option3" selected="true">by default</option>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	47 </param>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	48 <when value="option1">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	49 <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	50 </when>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	51 <when value="option2">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	52 <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	53 </when>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	54 <when value="option3">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	55 </when>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	56 </conditional>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	57 </inputs>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	58 <outputs>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	59 <data name="output" format="gro" label="${outname}"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	60 <data name="output_trr" format="trr" label="${outname_trr}"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	61 <data name="output_edr" format="edr" label="${outname_edr}"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	62 <data name="output_xtc" format="xtc" label="${outname_xtc}"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	63 <data name="output_cpt" format="cpt" label="${outname_cpt}"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	64 <data name="output_log" format="log" label="${outname_log}"/>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	65 </outputs>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	66 <tests>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	67 <test>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	68 </test>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	69 </tests>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	70 <help>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	71 .. class:: warningmark
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	72
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	73
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	74 Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	75
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	76 -----
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	77
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	78 .. image:: ${static_path}/images/biobb.png
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	79 :height: 57
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	80 :width: 150
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	81
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	82
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	83 https://bioexcel.eu
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	84 </help>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	85 <citations>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	86 <citation type="bibtex">
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	87 @misc{githubbiobb,
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	88 author = {Andrio P, Hospital A, Gelpi JL},
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	89 year = {2019},
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	90 title = {biobb: BioExcel building blocks },
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	91 publisher = {GitHub},
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	92 journal = {GitHub repository},
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	93 url = {https://github.com/bioexcel/biobb_io},
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	94 }</citation>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	95 </citations>
4c626e984fde Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	96 </tool>

2

4c626e984fde Uploaded