Mercurial > repos > chemteam > mdanalysis_rdf
comparison rdf.xml @ 4:36babbdd7818 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author | chemteam |
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date | Mon, 07 Oct 2019 12:51:57 -0400 |
parents | 57a3d6f94bcd |
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3:49dac57d004a | 4:36babbdd7818 |
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1 <tool id="mdanalysis_rdf" name="RDF Analysis" version="@VERSION@"> | 1 <tool id="mdanalysis_rdf" name="RDF Analysis" version="@VERSION@"> |
2 <description>Radial Distribution Function between two atoms</description> | 2 <description>- Radial Distribution Function between two atoms</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <command detect_errors="exit_code"> | 7 <command detect_errors="exit_code"> |
8 <![CDATA[ | 8 <![CDATA[ |
9 python '$__tool_directory__/rdf.py' | 9 python '$__tool_directory__/rdf.py' |
10 --idcd '$dcdin' | 10 --itraj '$trajin' |
11 --ipdb '$pdbin' | 11 --istr '$strin' |
12 --itrajext '$trajin.ext' | |
13 --istrext '$strin.ext' | |
12 --isegid1 '$segid1' | 14 --isegid1 '$segid1' |
13 --iresid1 '$resid1' | 15 --iresid1 '$resid1' |
14 --iname1 '$name1' | 16 --iname1 '$name1' |
15 --isegid2 '$segid2' | 17 --isegid2 '$segid2' |
16 --iresid2 '$resid2' | 18 --iresid2 '$resid2' |
22 --ordf_plot '$rdf_plot' | 24 --ordf_plot '$rdf_plot' |
23 2>&1 | 25 2>&1 |
24 ]]></command> | 26 ]]></command> |
25 <inputs> | 27 <inputs> |
26 <expand macro="analysis_inputs"/> | 28 <expand macro="analysis_inputs"/> |
27 <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/> | 29 <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/> |
28 <param name="resid1" type="text" value="212" label="Resid of atom 1"/> | 30 <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/> |
29 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/> | 31 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/> |
30 <param name="segid2" type="text" value="HET" label="Segid of atom 2"/> | 32 <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/> |
31 <param name="resid2" type="text" value="3" label="Resid of atom 2"/> | 33 <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/> |
32 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/> | 34 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/> |
33 <param name="nbins" type="text" value="100" label="Number of bins in the histogram"/> | 35 <param name="nbins" type="text" value="100" label="Number of bins in the histogram"/> |
34 <param name="start" type="text" value="0.0" label="Starting Point"/> | 36 <param name="start" type="text" min="0.0" value="0.0" label="Starting point (angstroms)" |
35 <param name="end" type="text" value="5.0" label="End Point"/> | 37 help="Minimum value of r to calculate RDF for"/> |
38 <param name="end" type="text" value="15.0" label="End point (angstroms)" | |
39 help="Maximum value of r to calculate RDF for"/> | |
36 </inputs> | 40 </inputs> |
37 <outputs> | 41 <outputs> |
38 <data format="tabular" name="output" label="RDF raw data"/> | 42 <data format="tabular" name="output" label="RDF raw data"/> |
39 <data format="png" name="rdf_plot" label="RDF Analysis Plot"/> | 43 <data format="png" name="rdf_plot" label="RDF Analysis Plot"/> |
40 </outputs> | 44 </outputs> |
56 <not_has_text text="nan" /> | 60 <not_has_text text="nan" /> |
57 <has_line_matching expression="3.625\s+5171.93.*" /> | 61 <has_line_matching expression="3.625\s+5171.93.*" /> |
58 </assert_contents> | 62 </assert_contents> |
59 </output> | 63 </output> |
60 </test> | 64 </test> |
65 <test> | |
66 <expand macro="tests_inputs_gmx"/> | |
67 <param name="segid1" value="SYSTEM"/> | |
68 <param name="resid1" value="212"/> | |
69 <param name="name1" value="OE2"/> | |
70 <param name="segid2" value="SYSTEM"/> | |
71 <param name="resid2" value="3"/> | |
72 <param name="name2" value="C1"/> | |
73 <param name="nbins" value="100"/> | |
74 <param name="start" value="0.0"/> | |
75 <param name="end" value="5.0"/> | |
76 <output name="output"> | |
77 <assert_contents> | |
78 <has_n_columns n="2" /> | |
79 <not_has_text text="nan" /> | |
80 <has_line_matching expression="3.275\s+6336.*" /> | |
81 </assert_contents> | |
82 </output> | |
83 </test> | |
61 </tests> | 84 </tests> |
62 <help><![CDATA[ | 85 <help><![CDATA[ |
63 .. class:: infomark | 86 .. class:: infomark |
64 | 87 |
65 **What it does** | 88 **What it does** |
66 | 89 |
67 The Radial Distribution Function (RDF) , g(r), also called pair distribution function or pair correlation function function can be used to find how density varies as a function of distance from a reference atom. | 90 The Radial Distribution Function (RDF), g(r), also called pair distribution function or pair correlation function, can be used to find how density varies as a function of distance from a reference atom. |
68 | 91 |
69 _____ | 92 _____ |
70 | 93 |
71 | 94 |
72 .. class:: infomark | 95 .. class:: infomark |
73 | 96 |
74 **Input** | 97 **Input** |
75 | 98 |
76 - Trajectory file (DCD). | 99 - Trajectory file (DCD). |
77 - PDB file. | 100 - PDB file. |
78 - Segids, resids and names of two atoms to calculate distances. | 101 - Segment IDs, residue IDs and names of two atoms to calculate RDF values. |
79 | 102 |
103 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system. | |
104 | |
105 Other parameters can also be specified: the number of bins in the RDF histogram, and the start and end points for the calculation (i.e. the values of r between which RDF will be calculated). | |
80 _____ | 106 _____ |
81 | 107 |
82 | 108 |
83 .. class:: infomark | 109 .. class:: infomark |
84 | 110 |