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comparison biobb_genrestr.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_genrestr" name="Genrestr" version="0.1.5" >
2 <description>: creates a new zip Gromacs topology applying the indicated force restrains</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 ${inputstr} ${inputstr}.${inputstr.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 genrestr --input_ndx_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} --input_structure_path ${inputstr}.${inputstr.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_top_zip_path $outputzip;
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} ${inputstr}.${inputstr.ext}
24 </command>
25 <inputs>
26 <param name="outnamezip" type="text" value="myGenrestr.zip" label="Output ZIP name" help="Name for the Output TOP topology. Format: [output].zip "/>
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"/>
28 <param name="inputname" type="data" format="ndx" label="Index file" help="Select your input GROMACS index file. Format: [input].ndx"/>
29 <param name="inputzip" type="data" format="zip" label="ZIP file" help="Select your input ZIP file. Format: [input].zip"/>
30 <conditional name="config">
31 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
32 <option value="option1">from configuration file</option>
33 <option value="option2">from JSON string</option>
34 <option value="option3" selected="true">by default</option>
35 </param>
36 <when value="option1">
37 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
38 </when>
39 <when value="option2">
40 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
41 </when>
42 <when value="option3">
43 </when>
44 </conditional>
45 </inputs>
46 <outputs>
47 <data name="outputzip" format="zip" label="${outnamezip}"/>
48 </outputs>
49 <tests>
50 <test>
51 </test>
52 </tests>
53 <help>
54 .. class:: warningmark
55
56
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
58
59 -----
60
61 .. image:: ${static_path}/images/biobb.png
62 :height: 57
63 :width: 150
64
65
66 **https://bioexcel.eu**
67 </help>
68 <citations>
69 <citation type="bibtex">
70 @misc{githubbiobb,
71 author = {Andrio P, Hospital A, Gelpi JL},
72 year = {2019},
73 title = {biobb: BioExcel building blocks },
74 publisher = {GitHub},
75 journal = {GitHub repository},
76 url = {https://github.com/bioexcel/biobb_io},
77 }</citation>
78 </citations>
79 </tool>