Mercurial > repos > chemteam > bio3d_pca_visualize

comparison visualize_pc.xml @ 3:f61a718993fd draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:44:04 -0400
parents 65bfd1b90b96
children
comparison
equal deleted inserted replaced
2:7ac6900f4790 3:f61a718993fd
1 <tool id="bio3d_pca_visualize" name="PCA visualization" version="@VERSION@"> 1 <tool id="bio3d_pca_visualize" name="PCA visualization" version="@VERSION@">
2 <description>Generate trajectories of principle components of motions</description> 2 <description>- generate trajectories of principal components of atomic motion</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
58 <expand macro="analysis_inputs"/> 58 <expand macro="analysis_inputs"/>
59 <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" 59 <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
60 label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" /> 60 label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" />
61 <conditional name="pca"> 61 <conditional name="pca">
62 <param name="sele" type="select" label="Select domains"> 62 <param name="sele" type="select" label="Select domains">
63 <option value="calpha">Calpha</option> 63 <option value="calpha">C-alpha</option>
64 <option value="cbeta">Cbeta</option> 64 <option value="cbeta">C-beta</option>
65 <option value="backbone">Backbone</option> 65 <option value="backbone">Backbone</option>
66 <option value="sidechain">Sidechain</option> 66 <option value="sidechain">Sidechain</option>
67 <option value="protein">Protein</option> 67 <option value="protein">Protein</option>
68 <option value="ligand">Ligand</option> 68 <option value="ligand">Ligand</option>
69 <option value="nucleic">Nucleic Acids</option> 69 <option value="nucleic">Nucleic acids</option>
70 <option value="elety">Atom Names</option> 70 <option value="elety">Atom names</option>
71 <option value="resid">Resid</option> 71 <option value="resid">Residue ID</option>
72 <option value="segid">Segid</option> 72 <option value="segid">Segment ID</option>
73 </param> 73 </param>
74 <when value="calpha"/> 74 <when value="calpha">
75 <when value="cbeta"/> 75 </when>
76 <when value="backbone"/> 76 <when value="cbeta">
77 <when value="sidechain"/> 77 </when>
78 <when value="protein"/> 78 <when value="backbone">
79 <when value="ligand"/> 79 </when>
80 <when value="nucleic"/> 80 <when value="sidechain">
81 <when value="elety"> 81 </when>
82 <param name="elety" type="text" value="CA" label="Atom Name"/> 82 <when value="protein">
83 </when> 83 </when>
84 <when value="resid"> 84 <when value="ligand">
85 <param name="resid" type="text" value="BGLC" label="Resid"/> 85 </when>
86 </when> 86 <when value="nucleic">
87 <when value="segid"> 87 </when>
88 <param name="segid" type="text" value="SUBS" label="Segid"/> 88 <when value="elety">
89 </when> 89 <param name="elety" type="text" value="CA" label="Atom name"/>
90 </when>
91 <when value="resid">
92 <param name="resid" type="text" value="BGLC" label="Residue ID"/>
93 </when>
94 <when value="segid">
95 <param name="segid" type="text" value="SUBS" label="Segment ID"/>
96 </when>
90 </conditional> 97 </conditional>
91 <param name="pc_id" type="integer" value="1" label="Principle component id"/> 98 <param name="pc_id" type="integer" value="1" label="Principal component ID"/>
92 </inputs> 99 </inputs>
100
93 <outputs> 101 <outputs>
94 <data format="pdb" name="pdbout" label="PCA_${pc_id}.pdb"/> 102 <data format="pdb" name="pdbout" label="PCA_${pc_id}.pdb"/>
95 </outputs> 103 </outputs>
96 <tests> 104 <tests>
97 <test> 105 <test>
105 <help><![CDATA[ 113 <help><![CDATA[
106 .. class:: infomark 114 .. class:: infomark
107 115
108 **What it does** 116 **What it does**
109 117
110 This tool can generate small trajectories of a given principle component. 118 This tool can generate small trajectories of a given principal component.
111 119
112 _____ 120 _____
113 121
114 122
115 .. class:: infomark 123 .. class:: infomark
116 124
117 **Input** 125 **Input**
118 126
119 - Input file in PDB format 127 - Input file in PDB format
120 - Input file in dcd format 128 - Input file in DCD format
121 129
122 _____ 130 _____
123 131
124 132
125 .. class:: infomark 133 .. class:: infomark
126 134
127 **Output** 135 **Output**
128 136
129 - A short trajectory (as PDB) of the given priciple component id. 137 - A short trajectory (as PDB) of the given principal component ID.
130 138
131 139
132 ]]></help> 140 ]]></help>
133 <expand macro="citations" /> 141 <expand macro="citations" />
134 </tool> 142 </tool>