Mercurial > repos > spanish_national_institue_of_bioinformatics > biobb

comparison biobb_mdrun.xml @ 2:4c626e984fde draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author spanish_national_institue_of_bioinformatics
date Fri, 12 Apr 2019 07:18:48 -0400
parents
children
comparison
equal deleted inserted replaced
1:21a0f28aea68 2:4c626e984fde
1 <tool id="biobb_mdrun" name="Mdrun" version="0.1.5" >
2 <description>: performs molecular dynamics simulations from an input Gromacs TPR file. </description>
3 <requirements>
4 <requirement type="binary">docker</requirement>
5 </requirements>
6 <command detect_errors="aggressive">
7 ln -f -s ${inputname} ${inputname}.${inputname.ext};
8 #if $config.sele == "option1":
9 ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
10 #end if
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}
12 #if $config.sele == "option1":
13 --config ${config.properties}.${config.properties.ext}
14 #else if $config.sele == "option2":
15 --config ${config.jsonstr}
16 #end if
17 --output_log_path $__root_dir__/database/files/000/$outname_log
18 --output_gro_path $__root_dir__/database/files/000/$outname
19 --output_trr_path $__root_dir__/database/files/000/$outname_trr
20 --output_edr_path $__root_dir__/database/files/000//$outname_edr
21 --output_xtc_path $__root_dir__/database/files/000/$outname_xtc
22 --output_cpt_path $__root_dir__/database/files/000/$outname_cpt;
23 #if $config.sele == "option1":
24 rm -f ${config.properties}.${config.properties.ext};
25 #end if
26 rm -f ${inputname}.${inputname.ext};
27 mv $__root_dir__/database/files/000/$outname $output;
28 mv $__root_dir__/database/files/000/$outname_trr $output_trr;
29 mv $__root_dir__/database/files/000//$outname_edr $output_edr;
30 mv $__root_dir__/database/files/000/$outname_xtc $output_xtc;
31 mv $__root_dir__/database/files/000/$outname_cpt $output_cpt;
32 mv $__root_dir__/database/files/000/$outname_log $output_log
33 </command>
34 <inputs>
35 <param name="inputname" type="data" format="tpr" label="TPR file" help="Select your portable binary run input file. Format: [input].tpr"/>
36 <param name="outname" type="text" value="mdrun.gro" label="Output GRO name" help="Name for the Output GROMACS structure. Format: [output].gro "/>
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"/>
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"/>
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"/>
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"/>
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"/>
42 <conditional name="config">
43 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
44 <option value="option1">from configuration file</option>
45 <option value="option2">from JSON string</option>
46 <option value="option3" selected="true">by default</option>
47 </param>
48 <when value="option1">
49 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
50 </when>
51 <when value="option2">
52 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
53 </when>
54 <when value="option3">
55 </when>
56 </conditional>
57 </inputs>
58 <outputs>
59 <data name="output" format="gro" label="${outname}"/>
60 <data name="output_trr" format="trr" label="${outname_trr}"/>
61 <data name="output_edr" format="edr" label="${outname_edr}"/>
62 <data name="output_xtc" format="xtc" label="${outname_xtc}"/>
63 <data name="output_cpt" format="cpt" label="${outname_cpt}"/>
64 <data name="output_log" format="log" label="${outname_log}"/>
65 </outputs>
66 <tests>
67 <test>
68 </test>
69 </tests>
70 <help>
71 .. class:: warningmark
72
73
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
75
76 -----
77
78 .. image:: ${static_path}/images/biobb.png
79 :height: 57
80 :width: 150
81
82
83 **https://bioexcel.eu**
84 </help>
85 <citations>
86 <citation type="bibtex">
87 @misc{githubbiobb,
88 author = {Andrio P, Hospital A, Gelpi JL},
89 year = {2019},
90 title = {biobb: BioExcel building blocks },
91 publisher = {GitHub},
92 journal = {GitHub repository},
93 url = {https://github.com/bioexcel/biobb_io},
94 }</citation>
95 </citations>
96 </tool>