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comparison rmsd.xml @ 0:75fd897bd85d draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
author chemteam
date Mon, 08 Oct 2018 12:49:59 -0400
parents
children 30cf714276b9
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-1:000000000000 0:75fd897bd85d
1 <tool id="bio3d_rmsd" name="RMSD Analysis" version="@VERSION@">
2 <description>RMSD using Bio3D</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 Rscript '$__tool_directory__/rmsd.R'
10 '$dcdin'
11 '$pdbin'
12 #if $rmsd.sele == 'calpha':
13 "string"
14 "calpha"
15 #end if
16 #if $rmsd.sele == 'cbeta':
17 "string"
18 "cbeta"
19 #end if
20 #if $rmsd.sele == 'backbone':
21 "string"
22 "backbone"
23 #end if
24 #if $rmsd.sele == 'sidechain':
25 "string"
26 "sidechain"
27 #end if
28 #if $rmsd.sele == 'protein':
29 "string"
30 "protein"
31 #end if
32 #if $rmsd.sele == 'ligand':
33 "string"
34 "ligand"
35 #end if
36 #if $rmsd.sele == 'nucleic':
37 "string"
38 "nucleic"
39 #end if
40 #if $rmsd.sele == 'water':
41 "string"
42 "water"
43 #end if
44 #if $rmsd.sele == 'hyd':
45 "string"
46 "hyd"
47 #end if
48 #if $rmsd.sele == 'noh':
49 "string"
50 "noh"
51 #end if
52 #if $rmsd.sele == "loop":
53 "resno"
54 '$rmsd.res1'
55 '$rmsd.res2'
56 #end if
57 #if $rmsd.sele == "elety":
58 "elety"
59 '$rmsd.elety'
60 #end if
61 #if $rmsd.sele == "resid":
62 "resid"
63 '$rmsd.resid'
64 #end if
65 #if $rmsd.sele == "segid":
66 "segid"
67 '$rmsd.segid'
68 #end if
69 '$output'
70 '$rmsd_plot'
71 '$rmsd_hist_plot'
72 2>&1
73 ]]></command>
74 <inputs>
75 <expand macro="analysis_inputs"/>
76 <conditional name="rmsd">
77 <param name="sele" type="select" label="Select domains">
78 <option value="calpha">Calpha</option>
79 <option value="cbeta">Cbeta</option>
80 <option value="backbone">Backbone</option>
81 <option value="sidechain">Sidechain</option>
82 <option value="protein">Protein</option>
83 <option value="ligand">Ligand</option>
84 <option value="nucleic">Nucleic Acids</option>
85 <option value="loop">Loop</option>
86 <option value="water">Water</option>
87 <option value="hyd">Hydrogens</option>
88 <option value="noh">Non Hydrogens</option>
89 <option value="elety">Atom Names</option>
90 <option value="resid">Resid</option>
91 <option value="segid">Segid</option>
92 </param>
93 <when value="calpha">
94 </when>
95 <when value="cbeta">
96 </when>
97 <when value="backbone">
98 </when>
99 <when value="sidechain">
100 </when>
101 <when value="protein">
102 </when>
103 <when value="ligand">
104 </when>
105 <when value="nucleic">
106 </when>
107 <when value="loop">
108 <param name="res1" type="text" label="Resid of the loop starting residue"/>
109 <param name="res2" type="text" label="Resid of the loop ending residue"/>
110 </when>
111 <when value="water">
112 </when>
113 <when value="hyd">
114 </when>
115 <when value="noh">
116 </when>
117 <when value="elety">
118 <param name="elety" type="text" value="CA" label="Atom Name"/>
119 </when>
120 <when value="resid">
121 <param name="resid" type="text" value="BGLC" label="Resid"/>
122 </when>
123 <when value="segid">
124 <param name="segid" type="text" value="SUBS" label="Segid"/>
125 </when>
126 </conditional>
127 </inputs>
128 <outputs>
129 <data format="tabular" name="output" label="RMSD raw data"/>
130 <data format="png" name="rmsd_plot" label="RMSD plot"/>
131 <data format="png" name="rmsd_hist_plot" label="RMSD Histogram Plot"/>
132 </outputs>
133 <tests>
134 <test>
135 <expand macro="tests_inputs"/>
136 <param name="sele" value="calpha"/>
137 <output name="output">
138 <assert_contents>
139 <has_n_columns n="2" />
140 </assert_contents>
141 </output>
142 </test>
143 </tests>
144 <help><![CDATA[
145
146 .. class:: infomark
147
148 **What it does**
149
150 The Root Mean Square Deviation (RMSD) is a standard measure of structural distance between coordinates.
151 This tool can calculate and plot the RMSD of the selected section.
152
153 _____
154
155
156 .. class:: infomark
157
158 **Input**
159
160 - Input file in PDB format
161 - Input file in DCD format
162
163 _____
164
165
166 .. class:: infomark
167
168 **Output**
169
170 - Image (as PNG) of the rmsd plot.
171 - Image (as PNG) of the rmsd histogram plot.
172 - Tab-separated file of raw data.
173
174 ]]></help>
175 <expand macro="citations" />
176 </tool>