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comparison distance.xml @ 0:c33b972fe040 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 13:16:12 -0400
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-1:000000000000 0:c33b972fe040
1 <tool id="mdanalysis_distance" name="Distance Analysis" version="@VERSION@">
2 <description>Time series using MDAnalysis</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 python '$__tool_directory__/distance.py'
10 --idcd '$dcdin'
11 --ipdb '$pdbin'
12 --isegid1 '$segid1'
13 --iresid1 '$resid1'
14 --iname1 '$name1'
15 --isegid2 '$segid2'
16 --iresid2 '$resid2'
17 --iname2 '$name2'
18 --output '$output'
19 --odistance_plot '$distance_plot'
20 2>&1
21 ]]></command>
22 <inputs>
23 <expand macro="analysis_inputs"/>
24 <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/>
25 <param name="resid1" type="text" value="212" label="Resid of atom 1"/>
26 <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"/>
28 <param name="resid2" type="text" value="3" label="Resid of atom 2"/>
29 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
30 </inputs>
31 <outputs>
32 <data format="tabular" name="output" label="Distance Analysis raw data"/>
33 <data format="png" name="distance_plot" label="Distance Analysis Plot"/>
34 </outputs>
35 <tests>
36 <test>
37 <expand macro="tests_inputs"/>
38 <param name="segid1" value="PRO"/>
39 <param name="resid1" value="212"/>
40 <param name="name1" value="OE2"/>
41 <param name="segid2" value="HET"/>
42 <param name="resid2" value="3"/>
43 <param name="name2" value="C1"/>
44 <output name="output">
45 <assert_contents>
46 <has_n_columns n="2" />
47 </assert_contents>
48 </output>
49 </test>
50 </tests>
51 <help><![CDATA[
52 .. class:: infomark
53
54 **What it does**
55
56 This tool calculates and plot distance between the two atoms.
57
58 _____
59
60
61 .. class:: infomark
62
63 **Input**
64
65 - Trajectory file (DCD).
66 - PDB file.
67 - Segids, resids and names of two atoms to calculate distances.
68
69 _____
70
71
72 .. class:: infomark
73
74 **Output**
75
76 - Tab-separated file of raw data of distance between two atoms calculated for each frame.
77 - Image (as png) of the time series graph.
78
79
80 ]]></help>
81 <expand macro="citations" />
82 </tool>