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comparison biobb_editconf.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_editconf" name="EditConf" version="0.1.5" >
2 <description>: creates a Gromacs file adding the information of the solvent box to the input</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 editconf --input_gro_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_gro_path $__root_dir__/database/files/000/$outname;
18 #if $config.sele == "option1":
19 rm -f ${config.properties}.${config.properties.ext};
20 #end if
21 rm -f ${inputname}.${inputname.ext};
22 mv $__root_dir__/database/files/000/$outname $output
23 </command>
24 <inputs>
25 <param name="outname" type="text" value="myEdit_conf.gro" label="Output GRO name" help="Name for the Output list. Format: [output].gro "/>
26 <param name="inputname" type="data" format="gro" label="Input GRO file" help="Select your input GRO file. Format: [input].gro"/>
27 <conditional name="config">
28 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
29 <option value="option1">from configuration file</option>
30 <option value="option2">from JSON string</option>
31 <option value="option3" selected="true">by default</option>
32 </param>
33 <when value="option1">
34 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
35 </when>
36 <when value="option2">
37 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
38 </when>
39 <when value="option3">
40 </when>
41
42 </conditional>
43 </inputs>
44 <outputs>
45 <data name="output" format="gro" label="${outname}"/>
46 </outputs>
47 <tests>
48 <test>
49 </test>
50 </tests>
51 <help>
52 .. class:: warningmark
53
54
55 Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.editconf
56
57 -----
58
59 .. image:: ${static_path}/images/biobb.png
60 :height: 57
61 :width: 150
62
63
64 **https://bioexcel.eu**
65 </help>
66 <citations>
67 <citation type="bibtex">
68 @misc{githubbiobb,
69 author = {Andrio P, Hospital A, Gelpi JL},
70 year = {2019},
71 title = {biobb: BioExcel building blocks },
72 publisher = {GitHub},
73 journal = {GitHub repository},
74 url = {https://github.com/bioexcel/biobb_io},
75 }</citation>
76 </citations>
77 </tool>