Mercurial > repos > chemteam > mdanalysis_cosine_analysis

annotate pca_cosine.xml @ 3:ff1e607d8b2b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 16:54:40 +0000
parents 9e77ecef62bf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
1 <tool id="mdanalysis_cosine_analysis" name="Cosine Content" version="@VERSION@">
1
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
2 <description>- measure the cosine content of the PCA projection</description>
0
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
3 <macros>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
4 <import>macros.xml</import>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
5 </macros>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
6 <expand macro="requirements" />
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
7 <command detect_errors="exit_code">
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
8 <![CDATA[
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
9 python '$__tool_directory__/pca_cosine.py'
1
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
10 --itraj '$trajin'
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
11 --istr '$strin'
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
12 --itrajext '$trajin.ext'
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
13 --istrext '$strin.ext'
0
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
14 --icomponents '$components'
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
15 --iindex '$index'
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
16 --output '$output'
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
17 --cosout '$cosout'
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
18 2>&1
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
19 ]]></command>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
20 <inputs>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
21 <expand macro="analysis_inputs"/>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
22 <param name="components" type="integer" value="3" label="Number of components"/>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
23 <param name="index" type="integer" value="0" label="The index of the PCA component projection to be analyzed"/>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
24 </inputs>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
25 <outputs>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
26 <data format="tabular" name="output" label="PCA Analysis raw data"/>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
27 <data format="txt" name="cosout" label="Cosine content of the PCA projection"/>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
28 </outputs>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
29 <tests>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
30 <test>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
31 <expand macro="tests_inputs"/>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
32 <param name="components" value="3"/>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
33 <param name="index" value="0"/>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
34 <output name="cosout">
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
35 <assert_contents>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
36 <has_text text="0.5832533" />
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
37 </assert_contents>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
38 </output>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
39 </test>
1
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
40 <test>
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
41 <expand macro="tests_inputs_gmx"/>
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
42 <param name="components" value="3"/>
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
43 <param name="index" value="0"/>
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
44 <output name="cosout">
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
45 <assert_contents>
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
46 <has_text text="0.583" />
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
47 </assert_contents>
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
48 </output>
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
49 </test>
0
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
50 </tests>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
51 <help><![CDATA[
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
52 .. class:: infomark
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
53
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
54 **What it does**
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
55
1
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
56 The cosine content of the principal components is a good indicator for determining the quality of the sampling and can be used to determine the convergence of the MD simulation.
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
57 This tool can calculate the cosine content of a user-defined PCA projection. Note: it uses zero-based indexes (i.e. 0 is the first principal component).
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
58
0
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
59 _____
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
60
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
61
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
62 .. class:: infomark
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
63
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
64 **Input**
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
65
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
66 - Trajectory file (DCD).
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
67 - PDB file.
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
68
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
69 _____
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
70
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
71
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
72 .. class:: infomark
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
73
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
74 **Output**
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
75
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
76 - The cosine content value.
1
9e77ecef62bf "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
77 - Tab-separated file of raw data of the first three principal components.
0
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
78
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
79 ]]></help>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
80 <expand macro="citations">
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
81 <citation type="doi">10.1103/PhysRevE.65.031910</citation>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
82 </expand>
ead44fe2be57 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
parents:
diff changeset
83 </tool>