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comparison biobb_pdb2gmx.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_pdb2gmx" name="Pdb2gmx" version="0.1.5" >
2 <description>: creates a ZIP Gromacs topology from a given PDB 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 pdb2gmx --input_pdb_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 --output_top_zip_path $outputzip;
19 #if $config.sele == "option1":
20 rm -f ${config.properties}.${config.properties.ext};
21 #end if
22 rm -f ${inputname}.${inputname.ext};
23 mv $__root_dir__/database/files/000/$outname $output
24 </command>
25 <inputs>
26 <param name="outname" type="text" value="myPdb2gmx.gro" label="Output GRO name" help="Name for the Output GRO. Format: [output].gro "/>
27 <param name="outzip" type="text" value="myPdb2gmx.zip" label="Output ZIP name" help="Name for the Output TOP topology. Format: [output].zip"/>
28 <param name="inputname" type="data" format="pdb" label="Input PDB file" help="Select your input PDB file. Format: [input].pdb"/>
29 <conditional name="config">
30 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
31 <option value="option1">from configuration file</option>
32 <option value="option2">from JSON string</option>
33 <option value="option3" selected="true">by default</option>
34 </param>
35 <when value="option1">
36 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
37 </when>
38 <when value="option2">
39 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
40 </when>
41 <when value="option3">
42 </when>
43
44 </conditional>
45 </inputs>
46 <outputs>
47 <data name="output" format="gro" label="${outname}"/>
48 <data name="outputzip" format="zip" label="${outzip}"/>
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.pdb2gmx
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>