Mercurial > repos > chemteam > mdanalysis_rdf

annotate rdf.xml @ 6:0f17d0720565 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 13:05:39 -0400
parents 36babbdd7818
children
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9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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1 <tool id="mdanalysis_rdf" name="RDF Analysis" version="@VERSION@">
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36babbdd7818 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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2 <description>- Radial Distribution Function between two atoms</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 python '$__tool_directory__/rdf.py'
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36babbdd7818 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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10 --itraj '$trajin'
36babbdd7818 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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11 --istr '$strin'
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12 --itrajext '$trajin.ext'
36babbdd7818 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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13 --istrext '$strin.ext'
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14 --isegid1 '$segid1'
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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15 --iresid1 '$resid1'
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16 --iname1 '$name1'
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17 --isegid2 '$segid2'
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18 --iresid2 '$resid2'
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19 --iname2 '$name2'
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20 --inbins '$nbins'
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21 --istart '$start'
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22 --iend '$end'
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23 --output '$output'
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24 --ordf_plot '$rdf_plot'
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25 2>&1
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26 ]]></command>
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27 <inputs>
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28 <expand macro="analysis_inputs"/>
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29 <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/>
36babbdd7818 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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30 <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/>
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31 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
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32 <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/>
36babbdd7818 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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33 <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/>
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34 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
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35 <param name="nbins" type="text" value="100" label="Number of bins in the histogram"/>
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36 <param name="start" type="text" min="0.0" value="0.0" label="Starting point (angstroms)"
36babbdd7818 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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37 help="Minimum value of r to calculate RDF for"/>
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38 <param name="end" type="text" value="15.0" label="End point (angstroms)"
36babbdd7818 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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39 help="Maximum value of r to calculate RDF for"/>
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40 </inputs>
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41 <outputs>
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42 <data format="tabular" name="output" label="RDF raw data"/>
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43 <data format="png" name="rdf_plot" label="RDF Analysis Plot"/>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <expand macro="tests_inputs"/>
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48 <param name="segid1" value="PRO"/>
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49 <param name="resid1" value="212"/>
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50 <param name="name1" value="OE2"/>
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51 <param name="segid2" value="HET"/>
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52 <param name="resid2" value="3"/>
2
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53 <param name="name2" value="C1"/>
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54 <param name="nbins" value="100"/>
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55 <param name="start" value="0.0"/>
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56 <param name="end" value="5.0"/>
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57 <output name="output">
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58 <assert_contents>
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59 <has_n_columns n="2" />
2
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60 <not_has_text text="nan" />
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61 <has_line_matching expression="3.625\s+5171.93.*" />
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62 </assert_contents>
2
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63 </output>
0
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64 </test>
4
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65 <test>
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66 <expand macro="tests_inputs_gmx"/>
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67 <param name="segid1" value="SYSTEM"/>
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68 <param name="resid1" value="212"/>
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69 <param name="name1" value="OE2"/>
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70 <param name="segid2" value="SYSTEM"/>
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71 <param name="resid2" value="3"/>
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72 <param name="name2" value="C1"/>
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73 <param name="nbins" value="100"/>
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74 <param name="start" value="0.0"/>
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75 <param name="end" value="5.0"/>
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76 <output name="output">
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77 <assert_contents>
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78 <has_n_columns n="2" />
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79 <not_has_text text="nan" />
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80 <has_line_matching expression="3.275\s+6336.*" />
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81 </assert_contents>
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82 </output>
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83 </test>
0
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84 </tests>
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85 <help><![CDATA[
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86 .. class:: infomark
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87
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88 **What it does**
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89
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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.
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91
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92 _____
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93
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94
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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95 .. class:: infomark
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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96
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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97 **Input**
9bb57bd1fdc8 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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98
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99 - Trajectory file (DCD).
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100 - PDB file.
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36babbdd7818 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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101 - Segment IDs, residue IDs and names of two atoms to calculate RDF values.
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102
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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.
36babbdd7818 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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104
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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).
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106 _____
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107
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108
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109 .. class:: infomark
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110
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111 **Output**
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112
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113 - Tab-separated file of raw data of the RDF.
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114 - Image (as png) of the RDF plot.
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115
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116 ]]></help>
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117 <expand macro="citations" />
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118 </tool>