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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna commit 6e51a331dbeab2786d8df5fd379ae3a63eb61d83
author rnateam
date Tue, 13 Dec 2016 11:47:56 -0500
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1 <tool id="remurna" name="remuRNA" version="1.0.0">
2 <description>Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation</description>
3 <requirements>
4 <requirement type="package" version="1.0">remurna</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command><![CDATA[
10 touch input.fa &&
11 python $__tool_directory__/create_input_file.py '$seq' '$snp' input.fa &&
12 \$(which remuRNA)
13 --proc="\${GALAXY_SLOTS}" ## number of CPUs
14 --window=$window
15 #if $advanced.advanced_selector =="advanced"
16 --NA=$advanced.NA
17 #if $advanced.energy == "abs_sig"
18 --energy='|sig|'
19 #else
20 --energy='sig'
21 #end if
22 --tmin=$advanced.tmin
23 --tinc=$advanced.tinc
24 --tmax=$advanced.tmax
25 #if $advanced.suffix
26 --suffix='$advanced.suffix'
27 #end if
28 --log=$advanced.log
29 #if $advanced.sodium
30 --sodium=$advanced.sodium
31 #end if
32 #if $advanced.magnesium
33 --magnesium=$advanced.magnesium
34 #end if
35 $advanced.polymer
36 $advanced.zip
37 $advanced.mutations
38 $advanced.nodangle
39 #end if
40 input.fa
41 > '$outfile'
42 ]]></command>
43 <inputs>
44 <param argument="--seq" type="data" format="fasta" label="Input Alignment File" />
45 <param argument="--snp" type="data" format="txt" label="SNP" help="remuRNA accepts only a single tag in each call."/>
46 <param argument="--window" type="integer" value="200" min="1" label="Windows size" help="Compute average distance over windows of size winsize."/>
47
48 <conditional name="advanced">
49 <param name="advanced_selector" type="select" label="Advanced Options">
50 <option value="basic">Basic options</option>
51 <option value="advanced">Advanced options</option>
52 </param>
53 <when value="basic"></when>
54 <when value="advanced">
55 <param argument="--NA" type="select" label="RNA or DNA">
56 <option value="RNA" selected="true">RNA sequence</option>
57 <option value="DNA">DNA sequence</option>
58 </param>
59 <param argument="--energy" type="select" label="Energy">
60 <option value="abs_sig" selected="true">|sig|</option>
61 <option value="sig">sig</option>
62 </param>
63
64 <param argument="--tmin" type="float" value="37.0" label="Min temperature [°C]" help=""/>
65 <param argument="--tmax" type="float" value="37.0" label="Max temperature [°C]" help=""/>
66 <param argument="--tinc" type="float" value="1.0" label="Temperature increment [°C]" help=""/>
67
68 <param argument="--suffix" type="text" optional="true" label="Suffix" />
69
70
71 <param argument="--sodium" type="float" optional="true" label="Salt concentration" help=""/>
72 <param argument="--magnesium" type="float" optional="true" label="Magnesium concentration" help=""/>
73 <param argument="--mutations" type="boolean" truevalue="--mutations" falsevalue="" checked="false" label="Compute relative entropy for all ppossible point mutations" help=""/>
74 <param argument="--nodangle" type="boolean" truevalue="" falsevalue="--nodangle" checked="true" label="Include dangling energies" help="default, dangling energies will be added for the bases adjacent to a helix on both sides in any case"/>
75 <param argument="--polymer" type="boolean" truevalue="--polymer" falsevalue="" checked="false" label="Polymer" help=""/>
76 <param argument="--zip" type="boolean" truevalue="--zip" falsevalue="" checked="false" label="Zip" help=""/>
77 <param argument="--log" type="select" label="Log level">
78 <option value="0">0: OFF</option>
79 <option value="1" selected="true">1: Errors</option>
80 <option value="2">2: Warnings</option>
81 <option value="3">3: Info</option>
82 <option value="4">4: Debug</option>
83 <option value="5">5: All</option>
84 </param>
85 </when>
86 </conditional>
87
88 </inputs>
89
90 <outputs>
91 <data name="outfile" format="tabular" />
92 </outputs>
93 <tests>
94 <test>
95 <param name="seq" value="seq.fa"/>
96 <param name="snp" value="snp.txt"/>
97 <output name="outfile" file="output.tabular"/>
98 </test>
99 </tests>
100 <help><![CDATA[
101 **What it does**
102
103 Measurement of Single-Nucleotide Polymorphism-induced Changes of RNA Conformation
104
105 Single-nucleotide polymorphisms (SNPs) are often linked to critical phenotypes such as diseases or responses to vaccines, medications and environmental factors. However, the specific molecular mechanisms by which a causal SNP acts is usually not obvious. Changes in RNA secondary structure emerge as a possible explanation necessitating the development of methods to measure the impact of single-nucleotide variation on RNA structure. To answer this need, remuRNA commutes the relative entropy between the Boltzmann ensembles of the native and a mutant structure.
106
107 **Input**
108
109 1. Sequence file: must contain one sequence in Fasta format.
110
111 2. SNP file: must contain only one tag
112
113
114 **Output**.
115
116 SNP MFE(wt) MFE(mu) dMFE H(wt||mu) GCratio
117
118 A23G -15.600 -16.000 0.400 0.877 0.336066
119 ]]></help>
120
121 <citations>
122 <citation type="doi">10.1093/nar/gks1009</citation>
123 </citations>
124 </tool>