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comparison biobb_grompp.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_grompp" name="Grompp" version="0.1.5" >
2 <description>:Gromacs preprocessor. Reads topology file to create TPR atomic description</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 ${inputgro} ${inputgro}.${inputgro.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 grompp --input_cpt_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} --input_gro_path ${inputgro}.${inputgro.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_tpr_path $__root_dir__/database/files/000/$outname;
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} ${inputgro}.${inputgro.ext};
24 mv $__root_dir__/database/files/000/$outname $output_tpr
25 </command>
26 <inputs>
27 <param name="inputgro" type="data" format="gro" label="Structure file" help="Select your input GROMACS structure file. Format: [input].gro"/>
28 <param name="inputzip" type="data" format="zip" label="Topology file" help="Select your input GROMACS topology TOP and ITP file. Format: [input].zip"/>
29 <param name="inputname" type="data" format="cpt" label="Check point file" optional="True" help="Select your input GROMACS checkpoint file. Format: [input].cpt"/>
30 <param name="outname" type="text" value="myGrompp.tpr" label="Output TPR name" help="Name for the Output binary run file. Format: [output].tpr "/>
31 <conditional name="config">
32 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
33 <option value="option1">from configuration file</option>
34 <option value="option2">from JSON string</option>
35 <option value="option3" selected="true">by default</option>
36 </param>
37 <when value="option1">
38 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
39 </when>
40 <when value="option2">
41 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
42 </when>
43 <when value="option3">
44 </when>
45 </conditional>
46 </inputs>
47 <outputs>
48 <data name="output_tpr" format="tpr" label="${outname}"/>
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.grompp
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>