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comparison rdf.xml @ 0:9bb57bd1fdc8 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
author chemteam
date Mon, 08 Oct 2018 13:17:18 -0400
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children 57a3d6f94bcd
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-1:000000000000 0:9bb57bd1fdc8
1 <tool id="mdanalysis_rdf" name="RDF Analysis" version="@VERSION@">
2 <description>Radial Distribution Function between two atoms</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 python '$__tool_directory__/rdf.py'
10 --idcd '$dcdin'
11 --ipdb '$pdbin'
12 --isegid1 '$segid1'
13 --iresid1 '$resid1'
14 --iname1 '$name1'
15 --isegid2 '$segid2'
16 --iresid2 '$resid2'
17 --iname2 '$name2'
18 --inbins '$nbins'
19 --istart '$start'
20 --iend '$end'
21 --output '$output'
22 --ordf_plot '$rdf_plot'
23 2>&1
24 ]]></command>
25 <inputs>
26 <expand macro="analysis_inputs"/>
27 <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/>
28 <param name="resid1" type="text" value="212" label="Resid of atom 1"/>
29 <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"/>
31 <param name="resid2" type="text" value="3" label="Resid of atom 2"/>
32 <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"/>
34 <param name="start" type="text" value="0.0" label="Starting Point"/>
35 <param name="end" type="text" value="5.0" label="End Point"/>
36 </inputs>
37 <outputs>
38 <data format="tabular" name="output" label="RDF raw data"/>
39 <data format="png" name="rdf_plot" label="RDF Analysis Plot"/>
40 </outputs>
41 <tests>
42 <test>
43 <expand macro="tests_inputs"/>
44 <param name="segid1" value="PRO"/>
45 <param name="resid1" value="212"/>
46 <param name="name1" value="OE2"/>
47 <param name="segid2" value="HET"/>
48 <param name="resid2" value="3"/>
49 <param name="name1" value="C1"/>
50 <param name="nbins" value="100"/>
51 <param name="start" value="0.0"/>
52 <param name="end" value="5.0"/>
53 <output name="output">
54 <assert_contents>
55 <has_n_columns n="2" />
56 </assert_contents>
57 </output>
58 </test>
59 </tests>
60 <help><![CDATA[
61 .. class:: infomark
62
63 **What it does**
64
65 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.
66
67 _____
68
69
70 .. class:: infomark
71
72 **Input**
73
74 - Trajectory file (DCD).
75 - PDB file.
76 - Segids, resids and names of two atoms to calculate distances.
77
78 _____
79
80
81 .. class:: infomark
82
83 **Output**
84
85 - Tab-separated file of raw data of the RDF.
86 - Image (as png) of the RDF plot.
87
88 ]]></help>
89 <expand macro="citations" />
90 </tool>