Mercurial > repos > spanish_national_institue_of_bioinformatics > biobb
comparison biobb_grompp.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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1:21a0f28aea68 | 2:4c626e984fde |
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1 <tool id="biobb_grompp" name="Grompp" version="0.1.5" > | |
2 <description>:Gromacs preprocessor. Reads topology file to create TPR atomic description</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 ${inputzip} ${inputzip}.${inputzip.ext}; | |
9 ln -f -s ${inputgro} ${inputgro}.${inputgro.ext}; | |
10 #if $config.sele == "option1": | |
11 ln -s -f ${config.properties} ${config.properties}.${config.properties.ext}; | |
12 #end if | |
13 docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 grompp --input_cpt_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} --input_gro_path ${inputgro}.${inputgro.ext} | |
14 #if $config.sele == "option1": | |
15 --config ${config.properties}.${config.properties.ext} | |
16 #else if $config.sele == "option2": | |
17 --config ${config.jsonstr} | |
18 #end if | |
19 --output_tpr_path $__root_dir__/database/files/000/$outname; | |
20 #if $config.sele == "option1": | |
21 rm -f ${config.properties}.${config.properties.ext}; | |
22 #end if | |
23 rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext} ${inputgro}.${inputgro.ext}; | |
24 mv $__root_dir__/database/files/000/$outname $output_tpr | |
25 </command> | |
26 <inputs> | |
27 <param name="inputgro" type="data" format="gro" label="Structure file" help="Select your input GROMACS structure file. Format: [input].gro"/> | |
28 <param name="inputzip" type="data" format="zip" label="Topology file" help="Select your input GROMACS topology TOP and ITP file. Format: [input].zip"/> | |
29 <param name="inputname" type="data" format="cpt" label="Check point file" optional="True" help="Select your input GROMACS checkpoint file. Format: [input].cpt"/> | |
30 <param name="outname" type="text" value="myGrompp.tpr" label="Output TPR name" help="Name for the Output binary run file. Format: [output].tpr "/> | |
31 <conditional name="config"> | |
32 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from"> | |
33 <option value="option1">from configuration file</option> | |
34 <option value="option2">from JSON string</option> | |
35 <option value="option3" selected="true">by default</option> | |
36 </param> | |
37 <when value="option1"> | |
38 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/> | |
39 </when> | |
40 <when value="option2"> | |
41 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/> | |
42 </when> | |
43 <when value="option3"> | |
44 </when> | |
45 </conditional> | |
46 </inputs> | |
47 <outputs> | |
48 <data name="output_tpr" format="tpr" label="${outname}"/> | |
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-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp | |
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> |