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comparison biobb_mutate.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_mutate" name="Mutate" version="0.1.5" >
2 <description>: mutate one aminoacid by another</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_model:0.1.5--py_0 mutate --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_pdb_path $output;
18 #if $config.sele == "option1":
19 rm -f ${config.properties}.${config.properties.ext};
20 #end if
21 rm -f ${inputname}.${inputname.ext}
22 </command>
23 <inputs>
24 <param name="outname" type="text" value="myMutate.pdb" label="Output PDB name" help="Name for the Output list. Format: [output].pdb "/>
25 <param name="inputname" type="data" format="pdb" label="Input PDB file" help="Select your input file. Format: [input].pdb"/>
26 <conditional name="config">
27 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
28 <option value="option1">from configuration file</option>
29 <option value="option2">from JSON string</option>
30 <option value="option3" selected="true">by default</option>
31 </param>
32 <when value="option1">
33 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
34 </when>
35 <when value="option2">
36 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
37 </when>
38 <when value="option3">
39 </when>
40
41 </conditional>
42 </inputs>
43 <outputs>
44 <data name="output" format="pdb" label="${outname}"/>
45 </outputs>
46 <tests>
47 <test>
48 </test>
49 </tests>
50 <help>
51 .. class:: warningmark
52
53
54 Check the syntax for setting the tool parameters at the original library documentation: https://biobb-model.readthedocs.io/en/latest/model.html#module-model.mutate
55
56 -----
57
58 .. image:: ${static_path}/images/biobb.png
59 :height: 57
60 :width: 150
61
62
63 **https://bioexcel.eu**
64 </help>
65 <citations>
66 <citation type="bibtex">
67 @misc{githubbiobb,
68 author = {Andrio P, Hospital A, Gelpi JL},
69 year = {2019},
70 title = {biobb: BioExcel building blocks },
71 publisher = {GitHub},
72 journal = {GitHub repository},
73 url = {https://github.com/bioexcel/biobb_io},
74 }</citation>
75 </citations>
76 </tool>