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comparison distance.xml @ 4:312f912de69d 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 12:52:40 -0400
parents 46892d756cec
children d540ea77b909
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3:489b25966bb9 4:312f912de69d
1 <tool id="mdanalysis_distance" name="Distance Analysis" version="@VERSION@"> 1 <tool id="mdanalysis_distance" name="Distance Analysis" version="@VERSION@">
2 <description>Time series using MDAnalysis</description> 2 <description>- time series using MDAnalysis</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 '$__tool_directory__/distance.py' 9 python '$__tool_directory__/distance.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'
19 --odistance_plot '$distance_plot' 21 --odistance_plot '$distance_plot'
20 2>&1 22 2>&1
21 ]]></command> 23 ]]></command>
22 <inputs> 24 <inputs>
23 <expand macro="analysis_inputs"/> 25 <expand macro="analysis_inputs"/>
24 <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/> 26 <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/>
25 <param name="resid1" type="text" value="212" label="Resid of atom 1"/> 27 <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/>
26 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/> 28 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
27 <param name="segid2" type="text" value="HET" label="Segid of atom 2"/> 29 <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/>
28 <param name="resid2" type="text" value="3" label="Resid of atom 2"/> 30 <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/>
29 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/> 31 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
30 </inputs> 32 </inputs>
31 <outputs> 33 <outputs>
32 <data format="tabular" name="output" label="Distance Analysis raw data"/> 34 <data format="tabular" name="output" label="Distance Analysis raw data"/>
33 <data format="png" name="distance_plot" label="Distance Analysis Plot"/> 35 <data format="png" name="distance_plot" label="Distance Analysis Plot"/>
41 <param name="segid2" value="HET"/> 43 <param name="segid2" value="HET"/>
42 <param name="resid2" value="3"/> 44 <param name="resid2" value="3"/>
43 <param name="name2" value="C1"/> 45 <param name="name2" value="C1"/>
44 <output name="output" file="Distance_Analysis_raw_data.tabular" /> 46 <output name="output" file="Distance_Analysis_raw_data.tabular" />
45 </test> 47 </test>
48 <test>
49 <expand macro="tests_inputs_gmx"/>
50 <param name="segid1" value="SYSTEM"/>
51 <param name="resid1" value="212"/>
52 <param name="name1" value="OE2"/>
53 <param name="segid2" value="SYSTEM"/>
54 <param name="resid2" value="3"/>
55 <param name="name2" value="C1"/>
56 <output name="output">
57 <assert_contents>
58 <has_n_columns n="2" />
59 <has_line_matching expression="0\s+3.8.*" />
60 <has_line_matching expression="14\s+3.2.*" />
61 </assert_contents>
62 </output>
63 </test>
46 </tests> 64 </tests>
47 <help><![CDATA[ 65 <help><![CDATA[
48 .. class:: infomark 66 .. class:: infomark
49 67
50 **What it does** 68 **What it does**
51 69
52 This tool calculates and plot distance between the two atoms. 70 This tool calculates and plots the distance between the two atoms.
53 71
54 _____ 72 _____
55 73
56 74
57 .. class:: infomark 75 .. class:: infomark
58 76
59 **Input** 77 **Input**
60 78
61 - Trajectory file (DCD). 79 - Trajectory file (DCD).
62 - PDB file. 80 - PDB file.
63 - Segids, resids and names of two atoms to calculate distances. 81 - Segment IDs, Residue IDs and names of two atoms to calculate distances.
64 82
83 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
84
65 _____ 85 _____
66 86
67 87
68 .. class:: infomark 88 .. class:: infomark
69 89