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

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author spanish_national_institue_of_bioinformatics
date Fri, 12 Apr 2019 07:18:48 -0400
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1:21a0f28aea68 2:4c626e984fde
1 <tool id="biobb_rms" name="RMS" version="0.1.3">
2 <description>: performs a RMSD analysis. </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 ln -f -s ${inputtraj} ${inputtraj}.${inputtraj.ext};
9 #if $config.sele == "option1":
10 ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
11 #end if
12 docker run -v $__root_dir__/database/files:$__root_dir__/database/files mmbirb/biobb_analysis:0.1.3 rms --input_structure_path $inputname.${inputname.ext} --input_traj_path ${inputtraj}.${inputtraj.ext}
13 #if $config.sele == "option1":
14 --config ${config.properties}.${config.properties.ext}
15 #else if $config.sele == "option2":
16 --config ${config.jsonstr}
17 #end if
18 --output_xvg_path $__root_dir__/database/files/000/$outname;
19 #if $config.sele == "option1":
20 rm -f ${config.properties}.${config.properties.ext};
21 #end if
22 rm -f ${inputname}.${inputname.ext} ${inputtraj}.${inputtraj.ext};
23 mv $__root_dir__/database/files/000/$outname $output
24 </command>
25 <inputs>
26 <param name="inputname" type="data" format="gro,pdb,tpr" label="Structure file" help="Select your input structure file. Format: [input].gro or [input].pdb or [input].tpr"/>
27 <param name="inputtraj" type="data" format="trr,xtc" label="Trajectory file" help="Select your input GROMACS trajectory. Format: [input].trr or [input].xtc"/>
28 <param name="outname" type="text" value="rms.xvg" label="Output XVG name" help="Name for the XVG Output. Format: [output].xvg "/>
29 <conditional name="config">
30 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
31 <option value="option1">from configuration file</option>
32 <option value="option2">from JSON string</option>
33 <option value="option3" selected="true">by default</option>
34 </param>
35 <when value="option1">
36 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
37 </when>
38 <when value="option2">
39 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
40 </when>
41 <when value="option3">
42 </when>
43
44 </conditional>
45 </inputs>
46 <outputs>
47 <data name="output" format="xvg" label="${outname}"/>
48
49 </outputs>
50 <tests>
51 <test>
52 </test>
53 </tests>
54 <help>
55 .. class:: warningmark
56
57
58 Check the syntax for setting the tool parameters at the original library documentation: https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.rms
59
60 -----
61
62 .. image:: ${static_path}/images/biobb.png
63 :height: 57
64 :width: 150
65
66
67 **https://bioexcel.eu**
68 </help>
69 <citations>
70 <citation type="bibtex">
71 @misc{githubbiobb,
72 author = {Andrio P, Hospital A, Gelpi JL},
73 year = {2019},
74 title = {biobb: BioExcel building blocks },
75 publisher = {GitHub},
76 journal = {GitHub repository},
77 url = {https://github.com/bioexcel/biobb_io},
78 }</citation>
79 </citations>
80 </tool>