Mercurial > repos > chemteam > mdanalysis_cosine_analysis
comparison pca_cosine.xml @ 0:ebeb72aa39a8 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author | chemteam |
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date | Wed, 03 Apr 2019 15:48:45 -0400 |
parents | |
children | d18e7db42633 |
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-1:000000000000 | 0:ebeb72aa39a8 |
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1 <tool id="mdanalysis_cosine_analysis" name="Cosine Content" version="@VERSION@"> | |
2 <description>Measure the cosine content of the PCA projection</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"> | |
8 <![CDATA[ | |
9 python '$__tool_directory__/pca_cosine.py' | |
10 --idcd '$dcdin' | |
11 --ipdb '$pdbin' | |
12 --icomponents '$components' | |
13 --iindex '$index' | |
14 --output '$output' | |
15 --cosout '$cosout' | |
16 2>&1 | |
17 ]]></command> | |
18 <inputs> | |
19 <expand macro="analysis_inputs"/> | |
20 <param name="components" type="integer" value="3" label="Number of components"/> | |
21 <param name="index" type="integer" value="0" label="The index of the PCA component projection to be analyzed"/> | |
22 </inputs> | |
23 <outputs> | |
24 <data format="tabular" name="output" label="PCA Analysis raw data"/> | |
25 <data format="txt" name="cosout" label="Cosine content of the PCA projection"/> | |
26 </outputs> | |
27 <tests> | |
28 <test> | |
29 <expand macro="tests_inputs"/> | |
30 <param name="components" value="3"/> | |
31 <param name="index" value="0"/> | |
32 <output name="cosout"> | |
33 <assert_contents> | |
34 <has_text text="0.5832533" /> | |
35 </assert_contents> | |
36 </output> | |
37 </test> | |
38 </tests> | |
39 <help><![CDATA[ | |
40 .. class:: infomark | |
41 | |
42 **What it does** | |
43 | |
44 The cosine content of the principal components is a good indicator for determine good or bad sampling and can be use to determine the convergence of the MD simulation. | |
45 This tool can calculate the cosine content of a user define PCA projection. | |
46 This tool use zero based indexes (0 is PC1). | |
47 | |
48 _____ | |
49 | |
50 | |
51 .. class:: infomark | |
52 | |
53 **Input** | |
54 | |
55 - Trajectory file (DCD). | |
56 - PDB file. | |
57 | |
58 _____ | |
59 | |
60 | |
61 .. class:: infomark | |
62 | |
63 **Output** | |
64 | |
65 - The cosine content value. | |
66 - Tab-separated file of raw data of first three principle component. | |
67 | |
68 ]]></help> | |
69 <expand macro="citations"> | |
70 <citation type="doi">10.1103/PhysRevE.65.031910</citation> | |
71 </expand> | |
72 </tool> |