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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
author rnateam
date Wed, 28 Dec 2016 18:52:45 -0500
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children 9942e1b7646c
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1 <tool id="locarna_reliability_profile" name="LocARNA reliability-profile" version="@VERSION@.0">
2 <description>
3 Plot reliability profile for probabilistic mlocarna
4 </description>
5
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9
10 <expand macro="requirements" />
11
12 <expand macro="stdio" />
13
14 <expand macro="version" />
15
16 <command><![CDATA[
17 (if file '$input_archive' | grep 'gzip compressed' > /dev/null ;
18 then tar xzf '$input_archive' ;
19 else tar xf '$input_archive' ;
20 fi)
21 &&
22 reliability-profile.pl mlocarna_results
23
24 --output-format='$output_format'
25
26 #if $output_format == 'pdf'
27 --out '$pdf_output_plot'
28 #else if $output_format == 'png'
29 --out '$png_output_plot'
30 #end if
31
32 #if str($title) != ""
33 --title '$title'
34 #end if
35
36 #if str($seqname) != ""
37 --seqname $seqname
38 #end if
39
40 --beta $beta
41 --structure-weight $structure_weight
42
43 #if str($signals)!=""
44 --signals '$signals'
45 #end if
46
47 --offset $offset
48
49 #if $write_rscript:
50 --write-R-script '$rscript_output'
51 #end if
52
53 #if $write_subsequence
54 --write-subseq
55 #end if
56
57 $predict
58 $fit_once_on
59 $show_sw
60 $rev_compl
61
62 > '$stdout'
63 ]]></command>
64
65 <inputs>
66 <param name="input_archive" type="data" format="tar.gz" label="MLocARNA archive"
67 help="Archive of MLocARNA results (tar or tar.gz as generated by running
68 mlocarna in probabilistic alignment mode)." />
69
70 <param name="title" type="text" label="Plot title"
71 help="Title of the plot"
72 />
73
74 <param name="seqname" type="text" label="Reference sequence"
75 help="Project to a reference sequence. Provide one of the sequence names in the alignment input
76 or leave blank to plot without projection."
77 />
78
79 <param name="predict" type="boolean" checked="True"
80 truevalue="" falsevalue="--dont-predict"
81 argument="dont-predict"
82 help="Turn on/off predicting."
83 />
84
85 <param name="fit_once_on" type="boolean" checked="False"
86 truevalue="--fit-once-on" falsevalue=""
87 argument="fit-once-on"
88 help="Predict exactly one 'on'-region"
89 />
90
91 <param name="show_sw" type="boolean" checked="True"
92 truevalue="--show-sw" falsevalue=""
93 argument="show-sw"
94 help="Show the influence of structure weight."
95 />
96
97 <param name="rev_compl" type="boolean" checked="False"
98 truevalue="--revcompl" falsevalue=""
99 argument="revcompl"
100 help="Plot and fit a reverse complement."
101 />
102
103 <param argument="beta" help="Inverse temperature for fitting."
104 type="float" value="12.0" min="1.0" max="25.0" />
105
106 <param name="structure_weight" argument="structure-weight"
107 type="float" value="1.0" min="0.0" max="8.0"
108 help="Weight of structure against sequence (1.0 means equal)"
109 />
110
111 <param argument="offset" help="Genomic offset."
112 type="integer" value="1" />
113
114 <param name="signals" type="text" label="List of signals"
115 help="List of '{from to} orientation' signal specifications. Show signals in plot
116 and compared infered signal to them. Ranges 'from to' can be repeated;
117 the orientation must be either +1 or -1.
118 The specifications of the single signals are separated by ';'. Example of two signal,
119 where the first one consists of two ranges: 1 15 20 30 +1; 15 45 -1"
120 >
121 <sanitizer invalid_char=" ">
122 <valid initial="string.digits"> <add value="+" /> <add value="-" /> <add value=";" /> </valid>
123 </sanitizer>
124 </param>
125
126 <param name="output_format" type="select"
127 label="Output options">
128 <option value="pdf" selected="True">Plot in pdf
129 format</option>
130 <option value="png" selected="False">Plot in png format</option>
131 </param>
132
133 <param name="write_rscript" type="boolean" argument="write-R-script"
134 label="Write R script" checked="False"
135 help="Write R script that can produce the output plot."
136 />
137
138 <param name="write_subsequence" type="boolean" argument="write-subseq"
139 label="Write Subsequence" checked="False"
140 help="Write subsequence in output."
141 />
142
143 </inputs>
144
145
146 <outputs>
147 <data format="pdf" name="pdf_output_plot"
148 label="${tool.name} reliability plot (pdf) ${on_string}">
149 <filter>output_format == 'pdf'</filter>
150 </data>
151 <data format="png" name="png_output_plot"
152 label="${tool.name} reliability plot (png) ${on_string}">
153 <filter>output_format == 'png'</filter>
154 </data>
155 <data format="txt" name="rscript_output"
156 label="${tool.name} reliability plot (R script) ${on_string}">
157 <filter> write_rscript is True </filter>
158 </data>
159 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}" />
160 </outputs>
161
162 <tests>
163 <test>
164 <param name="input_archive" value="archaea.tar.gz" />
165 <param name="write_rscript" value="True" />
166 <output name="rscript_output" file="archaea_relplot.scr" lines_diff="2" />
167 </test>
168 </tests>
169
170 <help><![CDATA[**Reliability Profiles for Multiple RNA
171 Alignment**
172
173 This tool draws reliability profiles for mlocarna alignments that have
174 been computed in probabilistic alignment mode. Moreover, it predicts
175 reliably aligned regions, which can be used to determine the
176 boundaries of well conserved structured RNA motifs in less closely
177 related sequence context.
178
179 **Input.**
180 Results archive of an alignment by the mlocarna tool; for this
181 purpose, mlocarna must be run in probabilistic mode in order to
182 generate the required reliability information.
183
184 **Output.**
185 Plot of the reliability profile for the input alignment. Moreover,
186 a signal prediction is performed and predicted regions are
187 annotated in the plot.
188
189
190 For more information, see
191 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
192 ]]></help>
193
194 <expand macro="citations" />
195
196 </tool>