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comparison rmsd.xml @ 5:77e28e1da9f4 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 12:44:25 -0400
parents 30cf714276b9
children
comparison
equal deleted inserted replaced
4:f871c9a8cb7c 5:77e28e1da9f4
1 <tool id="bio3d_rmsd" name="RMSD Analysis" version="@VERSION@"> 1 <tool id="bio3d_rmsd" name="RMSD Analysis" version="@VERSION@">
2 <description>RMSD using Bio3D</description> 2 <description> using Bio3D</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">
73 ]]></command> 73 ]]></command>
74 <inputs> 74 <inputs>
75 <expand macro="analysis_inputs"/> 75 <expand macro="analysis_inputs"/>
76 <conditional name="rmsd"> 76 <conditional name="rmsd">
77 <param name="sele" type="select" label="Select domains"> 77 <param name="sele" type="select" label="Select domains">
78 <option value="calpha">Calpha</option> 78 <option value="calpha">C-alpha</option>
79 <option value="cbeta">Cbeta</option> 79 <option value="cbeta">C-beta</option>
80 <option value="backbone">Backbone</option> 80 <option value="backbone">Backbone</option>
81 <option value="sidechain">Sidechain</option> 81 <option value="sidechain">Sidechain</option>
82 <option value="protein">Protein</option> 82 <option value="protein">Protein</option>
83 <option value="ligand">Ligand</option> 83 <option value="ligand">Ligand</option>
84 <option value="nucleic">Nucleic Acids</option> 84 <option value="nucleic">Nucleic acids</option>
85 <option value="loop">Loop</option> 85 <option value="loop">Loop</option>
86 <option value="water">Water</option> 86 <option value="water">Water</option>
87 <option value="hyd">Hydrogens</option> 87 <option value="hyd">Hydrogens</option>
88 <option value="noh">Non Hydrogens</option> 88 <option value="noh">Non-hydrogens</option>
89 <option value="elety">Atom Names</option> 89 <option value="elety">Atom names</option>
90 <option value="resid">Resid</option> 90 <option value="resid">Residue ID</option>
91 <option value="segid">Segid</option> 91 <option value="segid">Segment ID</option>
92 </param> 92 </param>
93 <when value="calpha"> 93 <when value="calpha">
94 </when> 94 </when>
95 <when value="cbeta"> 95 <when value="cbeta">
96 </when> 96 </when>
103 <when value="ligand"> 103 <when value="ligand">
104 </when> 104 </when>
105 <when value="nucleic"> 105 <when value="nucleic">
106 </when> 106 </when>
107 <when value="loop"> 107 <when value="loop">
108 <param name="res1" type="text" label="Resid of the loop starting residue"/> 108 <param name="res1" type="text" label="ID of the residue at the start of the loop"/>
109 <param name="res2" type="text" label="Resid of the loop ending residue"/> 109 <param name="res2" type="text" label="ID of the residue at the end of the loop"/>
110 </when> 110 </when>
111 <when value="water"> 111 <when value="water">
112 </when> 112 </when>
113 <when value="hyd"> 113 <when value="hyd">
114 </when> 114 </when>
115 <when value="noh"> 115 <when value="noh">
116 </when> 116 </when>
117 <when value="elety"> 117 <when value="elety">
118 <param name="elety" type="text" value="CA" label="Atom Name"/> 118 <param name="elety" type="text" value="CA" label="Atom name"/>
119 </when> 119 </when>
120 <when value="resid"> 120 <when value="resid">
121 <param name="resid" type="text" value="BGLC" label="Resid"/> 121 <param name="resid" type="text" value="BGLC" label="Residue ID"/>
122 </when> 122 </when>
123 <when value="segid"> 123 <when value="segid">
124 <param name="segid" type="text" value="SUBS" label="Segid"/> 124 <param name="segid" type="text" value="SUBS" label="Segment ID"/>
125 </when> 125 </when>
126 </conditional> 126 </conditional>
127 </inputs> 127 </inputs>
128 <outputs> 128 <outputs>
129 <data format="tabular" name="output" label="RMSD raw data"/> 129 <data format="tabular" name="output" label="RMSD raw data"/>
130 <data format="png" name="rmsd_plot" label="RMSD plot"/> 130 <data format="png" name="rmsd_plot" label="RMSD plot"/>
131 <data format="png" name="rmsd_hist_plot" label="RMSD Histogram Plot"/> 131 <data format="png" name="rmsd_hist_plot" label="RMSD histogram plot"/>
132 </outputs> 132 </outputs>
133 <tests> 133 <tests>
134 <test> 134 <test>
135 <expand macro="tests_inputs"/> 135 <expand macro="tests_inputs"/>
136 <param name="sele" value="calpha"/> 136 <param name="sele" value="calpha"/>
142 .. class:: infomark 142 .. class:: infomark
143 143
144 **What it does** 144 **What it does**
145 145
146 The Root Mean Square Deviation (RMSD) is a standard measure of structural distance between coordinates. 146 The Root Mean Square Deviation (RMSD) is a standard measure of structural distance between coordinates.
147 This tool can calculate and plot the RMSD of the selected section. 147 This tool can calculate and plot the RMSD of the selected section of the protein (or other molecule).
148 148
149 _____ 149 _____
150 150
151 151
152 .. class:: infomark 152 .. class:: infomark
161 161
162 .. class:: infomark 162 .. class:: infomark
163 163
164 **Output** 164 **Output**
165 165
166 - Image (as PNG) of the rmsd plot. 166 - Image (as PNG) of the RMSD plot.
167 - Image (as PNG) of the rmsd histogram plot. 167 - Image (as PNG) of the RMSD histogram plot.
168 - Tab-separated file of raw data. 168 - Tab-separated file of raw data.
169 169
170 ]]></help> 170 ]]></help>
171 <expand macro="citations" /> 171 <expand macro="citations" />
172 </tool> 172 </tool>