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comparison end-to-end.xml @ 0:78aa3659fcd1 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
author chemteam
date Mon, 24 Aug 2020 16:47:23 -0400
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1 <tool id="mdanalysis_endtoend" name="End-to-End Analysis" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>- End-to-End distance timeseries and histogram for the given selections</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code">
9 <![CDATA[
10 python '$__tool_directory__/end-to-end.py'
11 --itraj '$trajin'
12 --istr '$strin'
13 --itrajext '$trajin.ext'
14 --istrext '$strin.ext'
15 --isegid1 '$segid1'
16 --ilabel '$label1'
17 --ititle1 '$title1'
18 --output1 '$output1'
19 --o_plot '$o_plot'
20 2>&1
21 ]]></command>
22 <inputs>
23 <expand macro="analysis_inputs"/>
24 <param name="segid1" type="text" value="PROA" label="Segment ID of the protein" help="A valid segment ID selection for the current molecular system">
25 <validator type="regex" message="Maximum of 8 characters allowed.">^[a-zA-Z0-9]{1,8}$</validator>
26 </param>
27 <param name="label1" type="text" value="N-C" label="Data series label">
28 <validator type="regex" message="Maximum of 8 characters allowed.">^[a-zA-Z0-9\- ]{1,8}$</validator>
29 </param>
30 <param name="title1" type="text" value="End-to-End timeseries and histogram" label="Plot title" help="Plot title, to be included in image output">
31 <validator type="regex" message="Maximum of 36 characters allowed.">^[a-zA-Z0-9\- ]{1,36}$</validator>
32 </param>
33 </inputs>
34 <outputs>
35 <data format="tabular" name="output1" label="timeseries raw data"/>
36 <data format="png" name="o_plot" label="End-to-End Timeseries and Histogram Plot"/>
37 </outputs>
38 <tests>
39 <test>
40 <param name="trajin" value="test.dcd" ftype="dcd"/>
41 <param name="strin" value="test.pdb" ftype="pdb"/>
42 <param name="segid1" value="PRO"/>
43 <output name="output1">
44 <assert_contents>
45 <has_text text="3.921"/>
46 <has_text text="3.938"/>
47 </assert_contents>
48 </output>
49 <output name="o_plot">
50 <assert_contents>
51 <has_size value="39991" delta="3000"/>
52 </assert_contents>
53 </output>
54 </test>
55 </tests>
56 <help>
57 <![CDATA[
58 .. class:: infomark
59
60 **What it does**
61
62 End-to-End distance timeseries and histogram for proteins. The termini are chosen as ends with the N atom of the N-terminus and the C atom of the C-terminus chosen.
63
64 _____
65
66
67 .. class:: infomark
68
69 **Input**
70
71 - Trajectory file (DCD).
72 - PDB file.
73 - Segment ID for the protein
74 - Graph series label and title
75
76 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
77
78 _____
79
80
81 .. class:: infomark
82
83 **Output**
84
85 - Tab-separated file of timeseries raw data
86 - Image (as png) of the end-to-end timeseries and histogram
87
88 ]]>
89 </help>
90 <expand macro="citations"/>
91 </tool>