annotate biobb_grompp.xml @ 2:4c626e984fde draft default tip

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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>