Mercurial > repos > spanish_national_institue_of_bioinformatics > biobb

annotate biobb_ndx2resttop.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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
1 <tool id="biobb_ndx2resttop" name="Ndx2resttop" version="0.1.5" >
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
2 <description>: creates a Gromacs topology applying the force restrains</description>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
3 <requirements>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
4 <requirement type="binary">docker</requirement>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
5 </requirements>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
6 <command detect_errors="aggressive">
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
7 ln -f -s ${inputname} ${inputname}.${inputname.ext};
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
8 ln -f -s ${inputzip} ${inputzip}.${inputzip.ext};
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
9 #if $config.sele == "option1":
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
10 ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
11 #end if
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
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}
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
13 #if $config.sele == "option1":
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
14 --config ${config.properties}.${config.properties.ext}
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
15 #else if $config.sele == "option2":
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
16 --config ${config.jsonstr}
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
17 #end if
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
18 --output_top_zip_path $output;
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
19 #if $config.sele == "option1":
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
20 rm -f ${config.properties}.${config.properties.ext};
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
21 #end if
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
22 rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext}
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
23 </command>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
24 <inputs>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
25 <param name="outname" type="text" value="myNdx2resttop.zip" label="Output ZIP name" help="Name for the Output TOP topology. Format: [output].zip "/>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
26 <param name="inputname" type="data" format="ndx" label="Index file" help="Select your input index file. Format: [input].ndx"/>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
27 <param name="inputzip" type="data" format="zip" label="Input TOP file" help="Select your input TOP topology. Format: [input].zip"/>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
28 <conditional name="config">
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
29 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
30 <option value="option1">from configuration file</option>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
31 <option value="option2">from JSON string</option>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
32 <option value="option3" selected="true">by default</option>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
33 </param>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
34 <when value="option1">
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
35 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
36 </when>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
37 <when value="option2">
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
38 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
39 </when>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
40 <when value="option3">
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
41 </when>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
42
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
43 </conditional>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
44 </inputs>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
45 <outputs>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
46 <data name="output" format="zip" label="${outname}"/>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
47 </outputs>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
48 <tests>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
49 <test>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
50 </test>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
51 </tests>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
52 <help>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
53 .. class:: warningmark
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
54
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
55
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
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
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
57
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
58 -----
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
59
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
60 .. image:: ${static_path}/images/biobb.png
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
61 :height: 57
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
62 :width: 150
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
63
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
64
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
65 **https://bioexcel.eu**
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
66 </help>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
67 <citations>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
68 <citation type="bibtex">
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
69 @misc{githubbiobb,
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
70 author = {Andrio P, Hospital A, Gelpi JL},
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
71 year = {2019},
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
72 title = {biobb: BioExcel building blocks },
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
73 publisher = {GitHub},
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
74 journal = {GitHub repository},
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
75 url = {https://github.com/bioexcel/biobb_io},
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
76 }</citation>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
77 </citations>
4c626e984fde Uploaded
spanish_national_institue_of_bioinformatics
parents:
diff changeset
78 </tool>