Mercurial > repos > spanish_national_institue_of_bioinformatics > biobb

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author spanish_national_institue_of_bioinformatics
date Fri, 12 Apr 2019 07:18:48 -0400
parents
children
comparison
equal deleted inserted replaced
1:21a0f28aea68 2:4c626e984fde
1 <tool id="biobb_pdb" name="pdb" version="0.1.3" >
2 <description>: get PDB from rcsb.org</description>
3 <requirements>
4 <requirement type="binary">docker</requirement>
5 </requirements>
6 <command detect_errors="aggressive">
7 #if $config.sele == "option1":
8 ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
9 #end if
10 docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_io:0.1.3--py_0 pdb
11 #if $config.sele == "option1":
12 --config ${config.properties}.${config.properties.ext}
13 #else if $config.sele == "option2":
14 --config ${config.jsonstr}
15 #end if
16 --output_pdb_path $output;
17 #if $config.sele == "option1":
18 rm -f ${config.properties}.${config.properties.ext};
19 #end if
20 </command>
21 <inputs>
22 <param name="outname" type="text" value="myStructure.pdb" label="Output PDB name" help="Name for the Output list. Format: [output].pdb "/>
23 <conditional name="config">
24 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
25 <option value="option1">from configuration file</option>
26 <option value="option2">from JSON string</option>
27 <option value="option3" selected="true">by default</option>
28 </param>
29 <when value="option1">
30 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
31 </when>
32 <when value="option2">
33 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
34 </when>
35 <when value="option3">
36 </when>
37 </conditional>
38 </inputs>
39 <outputs>
40 <data name="output" format="pdb" label="${outname}"/>
41 </outputs>
42 <tests>
43 <test>
44 </test>
45 </tests>
46 <help>
47 .. class:: warningmark
48
49
50 Check the syntax for setting the tool parameters at the original library documentation: https://biobb-io.readthedocs.io/en/latest/mmb_api.html#module-mmb_api.pdb_variants
51
52 -----
53
54 .. image:: ${static_path}/images/biobb.png
55 :height: 57
56 :width: 150
57
58
59 **https://bioexcel.eu**
60 </help>
61 <citations>
62 <citation type="bibtex">
63 @misc{githubbiobb,
64 author = {Andrio P, Hospital A, Gelpi JL},
65 year = {2019},
66 title = {biobb: BioExcel building blocks },
67 publisher = {GitHub},
68 journal = {GitHub repository},
69 url = {https://github.com/bioexcel/biobb_io},
70 }</citation>
71 </citations>
72 </tool>