annotate biobb_ndx2resttop.xml @ 2:4c626e984fde draft default tip

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1 <tool id="biobb_ndx2resttop" name="Ndx2resttop" version="0.1.5" >
2     <description>: creates a Gromacs topology applying the force restrains</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     #if $config.sele == "option1":
10 	ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
11     #end if
12     docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 ndx2resttop --input_ndx_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext} 
13     #if $config.sele == "option1":
14 	--config ${config.properties}.${config.properties.ext}
15     #else if $config.sele == "option2":
16 	--config ${config.jsonstr}
17     #end if
18     --output_top_zip_path $output;
19     #if $config.sele == "option1":
20 	rm -f ${config.properties}.${config.properties.ext};
21     #end if
22     rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext}
23     </command>
24     <inputs>
25        <param name="outname" type="text" value="myNdx2resttop.zip" label="Output ZIP name" help="Name for the Output TOP topology. Format: [output].zip "/>
26        <param name="inputname" type="data" format="ndx"  label="Index file" help="Select your input index file. Format: [input].ndx"/>      
27        <param name="inputzip" type="data" format="zip"  label="Input TOP file" help="Select your input TOP topology. Format: [input].zip"/> 
28         <conditional name="config">
29 	    <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
30 	        <option value="option1">from configuration file</option>
31 	        <option value="option2">from JSON string</option>
32                 <option value="option3" selected="true">by default</option>
33 	    </param>
34 	    <when value="option1">
35 	        <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
36 	    </when>
37 	    <when value="option2">
38 	        <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
39 	    </when>
40 	    <when value="option3">
41 	    </when>
42        
43 	</conditional>
44     </inputs>
45     <outputs>
46    	<data name="output" format="zip" label="${outname}"/>
47     </outputs>
48     <tests>
49         <test>
50         </test>
51     </tests>
52     <help>
53 .. class:: warningmark
54 
55 
56 Check the syntax for setting the tool parameters at the original library documentation: https//biobb-md.readthedocs.io/en/latest/gromacs_extra.html#gromacs-extra-ndx2resttop-module 
57 
58 -----
59 
60 .. image:: ${static_path}/images/biobb.png
61     :height: 57
62     :width: 150
63 
64 
65 **https://bioexcel.eu**
66    </help>
67    <citations>
68         <citation type="bibtex">
69 @misc{githubbiobb,
70   author = {Andrio P, Hospital A, Gelpi JL},
71   year = {2019},
72   title = {biobb: BioExcel building blocks },
73   publisher = {GitHub},
74   journal = {GitHub repository},
75   url = {https://github.com/bioexcel/biobb_io},
76 }</citation>
77  </citations>
78 </tool>