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comparison rmsf.xml @ 0:e838317708a6 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 12:50:23 -0400
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children 057daf00ca31
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-1:000000000000 0:e838317708a6
1 <tool id="bio3d_rmsf" name="RMSF Analysis" version="@VERSION@">
2 <description>rmsf 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 '$__tool_directory__/rmsf.R'
10 '$dcdin'
11 '$pdbin'
12 #if $rmsf.sele == 'calpha':
13 "string"
14 "calpha"
15 #end if
16 #if $rmsf.sele == 'cbeta':
17 "string"
18 '$rmsf.cbeta'
19 #end if
20 #if $rmsf.sele == 'backbone':
21 "string"
22 "backbone"
23 #end if
24 #if $rmsf.sele == 'sidechain':
25 "string"
26 '$rmsf.sidechain'
27 #end if
28 #if $rmsf.sele == 'protein':
29 "string"
30 "protein"
31 #end if
32 #if $rmsf.sele == 'ligand':
33 "string"
34 "ligand"
35 #end if
36 #if $rmsf.sele == 'nucleic':
37 "string"
38 "nucleic"
39 #end if
40 #if $rmsf.sele == 'water':
41 "string"
42 "water"
43 #end if
44 #if $rmsf.sele == 'hyd':
45 "string"
46 "hyd"
47 #end if
48 #if $rmsf.sele == 'noh':
49 "string"
50 "noh"
51 #end if
52 #if $rmsf.sele == 'loop':
53 "resno"
54 '$rmsf.res1'
55 '$rmsf.res2'
56 #end if
57 #if $rmsf.sele == "elety":
58 "elety"
59 '$rmsf.elety'
60 #end if
61 #if $rmsf.sele == "resid":
62 "resid"
63 '$rmsf.resid'
64 #end if
65 #if $rmsf.sele == "segid":
66 "segid"
67 '$rmsf.segid'
68 #end if
69 '$output'
70 '$rmsf_plot'
71 2>&1
72 ]]></command>
73 <inputs>
74 <expand macro="analysis_inputs"/>
75 <conditional name="rmsf">
76 <param name="sele" type="select" label="Select domains">
77 <option value="calpha">Calpha</option>
78 <option value="cbeta">Cbeta</option>
79 <option value="backbone">Backbone</option>
80 <option value="sidechain">Sidechain</option>
81 <option value="protein">Protein</option>
82 <option value="ligand">Ligand</option>
83 <option value="nucleic">Nucleic Acids</option>
84 <option value="loop">Loop</option>
85 <option value="water">Water</option>
86 <option value="hyd">Hydrogens</option>
87 <option value="noh">Non Hydrogens</option>
88 <option value="elety">Atom Names</option>
89 <option value="resid">Resid</option>
90 <option value="segid">Segid</option>
91 </param>
92 <when value="calpha">
93 </when>
94 <when value="cbeta">
95 </when>
96 <when value="backbone">
97 </when>
98 <when value="sidechain">
99 </when>
100 <when value="protein">
101 </when>
102 <when value="ligand">
103 </when>
104 <when value="nucleic">
105 </when>
106 <when value="loop">
107 <param name="res1" type="text" label="Resid of the loop starting residue"/>
108 <param name="res2" type="text" label="Resid of the loop ending residue"/>
109 </when>
110 <when value="water">
111 </when>
112 <when value="hyd">
113 </when>
114 <when value="noh">
115 </when>
116 <when value="elety">
117 <param name="elety" type="text" value="CA" label="Atom Name"/>
118 </when>
119 <when value="resid">
120 <param name="resid" type="text" value="BGLC" label="Resid"/>
121 </when>
122 <when value="segid">
123 <param name="segid" type="text" value="SUBS" label="Segid"/>
124 </when>
125 </conditional>
126 </inputs>
127 <outputs>
128 <data format="tabular" name="output" label="rmsf raw data"/>
129 <data format="png" name="rmsf_plot" label="rmsf plot"/>
130 </outputs>
131 <tests>
132 <test>
133 <expand macro="tests_inputs"/>
134 <param name="sele" value="calpha"/>
135 <output name="output">
136 <assert_contents>
137 <has_n_columns n="2" />
138 </assert_contents>
139 </output>
140 </test>
141 </tests>
142 <help><![CDATA[
143
144 .. class:: infomark
145
146 **What it does**
147
148 The Root Mean Square Fluctuation (RMSF) conformational variance that analysis can analyze the
149 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.
150
151 _____
152
153 .. class:: infomark
154
155 **Input**
156
157 - Input file in PDB format
158 - Input file in DCD format
159
160 _____
161
162 .. class:: infomark
163
164 **Output**
165
166 - Image (as PNG) of the rmsf plot
167 - Tab-separated file of raw data
168
169
170 ]]></help>
171 <expand macro="citations" />
172 </tool>