Mercurial > repos > chemteam > bio3d_pca_visualize

annotate visualize_pc.xml @ 1:0692d9f9edd3 draft

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/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
author chemteam
date Wed, 27 Mar 2019 15:17:42 -0400
parents 65bfd1b90b96
children f61a718993fd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
1 <tool id="bio3d_pca_visualize" name="PCA visualization" version="@VERSION@">
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
2 <description>Generate trajectories of principle components of motions</description>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
3 <macros>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
4 <import>macros.xml</import>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
5 </macros>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
6 <expand macro="requirements" />
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
7 <command detect_errors="exit_code">
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
8 <![CDATA[
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
9 Rscript '$__tool_directory__/visualize_pc.R'
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
10 '$dcdin'
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
11 '$pdbin'
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
12 '$method'
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
13 #if $pca.sele == 'calpha':
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
14 "string"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
15 "calpha"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
16 #end if
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
17 #if $pca.sele == 'cbeta':
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
18 "string"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
19 '$pca.cbeta'
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
20 #end if
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
21 #if $pca.sele == 'backbone':
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
22 "string"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
23 "backbone"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
24 #end if
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
25 #if $pca.sele == 'sidechain':
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
26 "string"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
27 "sidechain"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
28 #end if
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
29 #if $pca.sele == 'protein':
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
30 "string"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
31 "protein"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
32 #end if
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
33 #if $pca.sele == 'ligand':
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
34 "string"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
35 "ligand"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
36 #end if
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
37 #if $pca.sele == 'nucleic':
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
38 "string"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
39 "nucleic"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
40 #end if
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
41 #if $pca.sele == 'elety':
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
42 "elety"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
43 '$pca.elety'
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
44 #end if
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
45 #if $pca.sele == 'resid':
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
46 "resid"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
47 '$pca.resid'
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
48 #end if
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
49 #if $pca.sele == 'segid':
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
50 "segid"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
51 '$pca.segid'
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
52 #end if
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
53 '$pc_id'
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
54 '$pdbout'
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
55 2>&1
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
56 ]]></command>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
57 <inputs>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
58 <expand macro="analysis_inputs"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
59 <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
60 label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" />
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
61 <conditional name="pca">
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
62 <param name="sele" type="select" label="Select domains">
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
63 <option value="calpha">Calpha</option>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
64 <option value="cbeta">Cbeta</option>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
65 <option value="backbone">Backbone</option>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
66 <option value="sidechain">Sidechain</option>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
67 <option value="protein">Protein</option>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
68 <option value="ligand">Ligand</option>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
69 <option value="nucleic">Nucleic Acids</option>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
70 <option value="elety">Atom Names</option>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
71 <option value="resid">Resid</option>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
72 <option value="segid">Segid</option>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
73 </param>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
74 <when value="calpha"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
75 <when value="cbeta"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
76 <when value="backbone"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
77 <when value="sidechain"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
78 <when value="protein"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
79 <when value="ligand"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
80 <when value="nucleic"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
81 <when value="elety">
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
82 <param name="elety" type="text" value="CA" label="Atom Name"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
83 </when>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
84 <when value="resid">
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
85 <param name="resid" type="text" value="BGLC" label="Resid"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
86 </when>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
87 <when value="segid">
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
88 <param name="segid" type="text" value="SUBS" label="Segid"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
89 </when>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
90 </conditional>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
91 <param name="pc_id" type="integer" value="1" label="Principle component id"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
92 </inputs>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
93 <outputs>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
94 <data format="pdb" name="pdbout" label="PCA_${pc_id}.pdb"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
95 </outputs>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
96 <tests>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
97 <test>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
98 <expand macro="tests_inputs"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
99 <param name="method" value="false"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
100 <param name="sele" value="calpha"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
101 <param name="pc_id" value="1"/>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
102 <output name="pdbout" file="PCA_1.pdb" />
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
103 </test>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
104 </tests>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
105 <help><![CDATA[
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
106 .. class:: infomark
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
107
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
108 **What it does**
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
109
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
110 This tool can generate small trajectories of a given principle component.
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
111
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
112 _____
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
113
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
114
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
115 .. class:: infomark
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
116
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
117 **Input**
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
118
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
119 - Input file in PDB format
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
120 - Input file in dcd format
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
121
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
122 _____
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
123
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
124
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
125 .. class:: infomark
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
126
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
127 **Output**
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
128
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
129 - A short trajectory (as PDB) of the given priciple component id.
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
130
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
131
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
132 ]]></help>
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
133 <expand macro="citations" />
65bfd1b90b96 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
chemteam
parents:
diff changeset
134 </tool>