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comparison rdf.xml @ 4:36babbdd7818 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:51:57 -0400
parents 57a3d6f94bcd
children
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3:49dac57d004a 4:36babbdd7818
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