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comparison rmsf.xml @ 5:6bcb804a54c3 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 12:45:26 -0400
parents 057daf00ca31
children
comparison
equal deleted inserted replaced
4:4354d92dc1aa 5:6bcb804a54c3
1 <tool id="bio3d_rmsf" name="RMSF Analysis" version="@VERSION@"> 1 <tool id="bio3d_rmsf" name="RMSF Analysis" version="@VERSION@">
2 <description>rmsf 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">
72 ]]></command> 72 ]]></command>
73 <inputs> 73 <inputs>
74 <expand macro="analysis_inputs"/> 74 <expand macro="analysis_inputs"/>
75 <conditional name="rmsf"> 75 <conditional name="rmsf">
76 <param name="sele" type="select" label="Select domains"> 76 <param name="sele" type="select" label="Select domains">
77 <option value="calpha">Calpha</option> 77 <option value="calpha">C-alpha</option>
78 <option value="cbeta">Cbeta</option> 78 <option value="cbeta">C-beta</option>
79 <option value="backbone">Backbone</option> 79 <option value="backbone">Backbone</option>
80 <option value="sidechain">Sidechain</option> 80 <option value="sidechain">Sidechain</option>
81 <option value="protein">Protein</option> 81 <option value="protein">Protein</option>
82 <option value="ligand">Ligand</option> 82 <option value="ligand">Ligand</option>
83 <option value="nucleic">Nucleic Acids</option> 83 <option value="nucleic">Nucleic acids</option>
84 <option value="loop">Loop</option> 84 <option value="loop">Loop</option>
85 <option value="water">Water</option> 85 <option value="water">Water</option>
86 <option value="hyd">Hydrogens</option> 86 <option value="hyd">Hydrogens</option>
87 <option value="noh">Non Hydrogens</option> 87 <option value="noh">Non-hydrogens</option>
88 <option value="elety">Atom Names</option> 88 <option value="elety">Atom names</option>
89 <option value="resid">Resid</option> 89 <option value="resid">Residue ID</option>
90 <option value="segid">Segid</option> 90 <option value="segid">Segment ID</option>
91 </param> 91 </param>
92 <when value="calpha"> 92 <when value="calpha">
93 </when> 93 </when>
94 <when value="cbeta"> 94 <when value="cbeta">
95 </when> 95 </when>
102 <when value="ligand"> 102 <when value="ligand">
103 </when> 103 </when>
104 <when value="nucleic"> 104 <when value="nucleic">
105 </when> 105 </when>
106 <when value="loop"> 106 <when value="loop">
107 <param name="res1" type="text" label="Resid of the loop starting residue"/> 107 <param name="res1" type="text" label="ID of the residue at the start of the loop"/>
108 <param name="res2" type="text" label="Resid of the loop ending residue"/> 108 <param name="res2" type="text" label="ID of the residue at the end of the loop"/>
109 </when> 109 </when>
110 <when value="water"> 110 <when value="water">
111 </when> 111 </when>
112 <when value="hyd"> 112 <when value="hyd">
113 </when> 113 </when>
114 <when value="noh"> 114 <when value="noh">
115 </when> 115 </when>
116 <when value="elety"> 116 <when value="elety">
117 <param name="elety" type="text" value="CA" label="Atom Name"/> 117 <param name="elety" type="text" value="CA" label="Atom name"/>
118 </when> 118 </when>
119 <when value="resid"> 119 <when value="resid">
120 <param name="resid" type="text" value="BGLC" label="Resid"/> 120 <param name="resid" type="text" value="BGLC" label="Residue ID"/>
121 </when> 121 </when>
122 <when value="segid"> 122 <when value="segid">
123 <param name="segid" type="text" value="SUBS" label="Segid"/> 123 <param name="segid" type="text" value="SUBS" label="Segment ID"/>
124 </when> 124 </when>
125 </conditional> 125 </conditional>
126 </inputs> 126 </inputs>
127 <outputs> 127 <outputs>
128 <data format="tabular" name="output" label="rmsf raw data"/> 128 <data format="tabular" name="output" label="RMSF raw data"/>
129 <data format="png" name="rmsf_plot" label="rmsf plot"/> 129 <data format="png" name="rmsf_plot" label="RMSF plot"/>
130 </outputs> 130 </outputs>
131 <tests> 131 <tests>
132 <test> 132 <test>
133 <expand macro="tests_inputs"/> 133 <expand macro="tests_inputs"/>
134 <param name="sele" value="calpha"/> 134 <param name="sele" value="calpha"/>
135 <output name="output" file="rmsf_raw_data.tabular" /> 135 <output name="output" >
136 <assert_contents>
137 <has_line_matching expression="1\t0.297.*" />
138 <has_line_matching expression="418\t0.410.*" />
139 <has_line_matching expression="433\t0.300.*" />
140 </assert_contents>
141 </output>
136 </test> 142 </test>
137 </tests> 143 </tests>
138 <help><![CDATA[ 144 <help><![CDATA[
139 145
140 .. class:: infomark 146 .. class:: infomark
141 147
142 **What it does** 148 **What it does**
143 149
144 The Root Mean Square Fluctuation (RMSF) conformational variance that analysis can analyze the 150 The Root Mean Square Fluctuation (RMSF) provides a measure of conformational variance i.e. which
145 portions of structure that are fluctuating from their mean structure the most (or least). This tool can calculate and plot the RMSF of the selected section. 151 portions of structure are fluctuating from their mean structure the most (or least).
152 This tool can calculate and plot the RMSF of the selected section of the protein (or other molecule).
146 153
147 _____ 154 _____
148 155
149 .. class:: infomark 156 .. class:: infomark
150 157
157 164
158 .. class:: infomark 165 .. class:: infomark
159 166
160 **Output** 167 **Output**
161 168
162 - Image (as PNG) of the rmsf plot 169 - Image (as PNG) of the RMSF plot
163 - Tab-separated file of raw data 170 - Tab-separated file of raw data
164 171
165 172
166 ]]></help> 173 ]]></help>
167 <expand macro="citations" /> 174 <expand macro="citations" />