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comparison rnaz.xml @ 1:e23c455f8335 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
author bgruening
date Wed, 01 Mar 2017 17:15:13 -0500
parents 8abf4c0a4af0
children 580ee1e91801
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0:8abf4c0a4af0 1:e23c455f8335
1 <tool id="rnaz" name="RNAz" version="0.1.0"> 1 <tool id="rnaz" name="RNAz" version="2.1.0">
2 <description>predicting structurally conserved and thermodynamically stable RNA secondary structures</description> 2 <description>predicting structurally conserved and thermodynamically stable RNA secondary structures</description>
3 <version_command>RNAz --version</version_command> 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.1">rnaz</requirement> 5 <requirement type="package" version="2.1">rnaz</requirement>
6 </requirements> 6 </requirements>
7 <command> 7
8 RNAz $input
9 $forward
10 $reverse
11 $both_strands
12 $dinucleotide
13 $mononucleotide
14 $locarnate
15 $no_shuffle
16 #if $cutoff_p != -1:
17 --cutoff=$cutoff_p
18 #end if
19 &gt; temp.txt;
20 grep -v -E "^ |^#|^$" temp.txt &gt; $outfile;
21 grep -E "^ |^#|^$" temp.txt;
22 </command>
23 <stdio> 8 <stdio>
24 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 9 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
25 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 10 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
26 </stdio> 11 </stdio>
12
13 <version_command>RNAz --version</version_command>
14 <command>
15 <![CDATA[
16 RNAz '$input'
17 --$forward_or_reverse
18 $dinucleotide
19 $mononucleotide
20 $locarnate
21 $noshuffle
22 #if $cutoff != -1.0:
23 --cutoff=$cutoff
24 #end if
25 > temp.txt &&
26 grep -v -E "^ |^#|^$" temp.txt > '$outfile' &&
27 grep -E "^ |^#|^$" temp.txt
28 ]]>
29 </command>
27 <inputs> 30 <inputs>
28 <param format="txt" name="input" type="data" label="Input Alignment File" /> 31 <param format="txt" name="input" type="data" label="Input Alignment File" />
29 <param name="forward" type="boolean" checked="false" truevalue="--forward" falsevalue="" label="Score forward strand" help="--forward" /> 32 <param name="forward_or_reverse" type="select" label="Scored strand">
30 <param name="reverse" type="boolean" checked="false" truevalue="--reverse" falsevalue="" label="Score reverse strand" help="--reverse" /> 33 <option value="forward">Score forward strand (-f)</option>
31 <param name="both_strands" type="boolean" checked="false" truevalue="-e" falsevalue="" label="Score both strands" help="-e" /> 34 <option value="reverse">Score reverse strand (-r)</option>
32 <param name="cutoff_p" label="Probability cutoff" type="float" value="-1" help="-1 to deactivate"/> 35 <option value="both-strands">Score both strands (-b)</option>
33 <param name="dinucleotide" type="boolean" checked="true" truevalue="--dinucleotide" falsevalue="" label="Use dinucleotide shuffled z-scores" help="--dinucleotide" /> 36 </param>
34 <param name="mononucleotide" type="boolean" checked="true" truevalue="--mononucleotide" falsevalue="" label="Use mononucleotide shuffled z-scores" help="--mononucleotide" /> 37 <param argument="--cutoff" label="Probability cutoff" type="float" value="-1.0" help="-1.0 to deactivate"/>
35 <param name="locarnate" type="boolean" checked="false" truevalue="--locarnate" falsevalue="" label="Use decision model for structural alignments" help="--locarnate" /> 38 <param argument="--dinucleotide" type="boolean" checked="true" truevalue="--dinucleotide" falsevalue="" label="Use dinucleotide shuffled z-scores" />
36 <param name="no_shuffle" type="boolean" checked="false" truevalue="--no-shuffle" falsevalue="" label="Never fall back to shuffling" help="--no-shuffle" /> 39 <param argument="--mononucleotide" type="boolean" checked="true" truevalue="--mononucleotide" falsevalue="" label="Use mononucleotide shuffled z-scores" />
40 <param argument="--locarnate" type="boolean" checked="false" truevalue="--locarnate" falsevalue="" label="Use decision model for structural alignments" />
41 <param argument="--no-shuffle" name="noshuffle" type="boolean" checked="false" truevalue="--no-shuffle" falsevalue="" label="Never fall back to shuffling" />
37 </inputs> 42 </inputs>
38 <outputs> 43 <outputs>
39 <data name="outfile" format="fasta" /> 44 <data name="outfile" format="fasta" />
40 </outputs> 45 </outputs>
41 <help>**What it does** 46 <tests>
42 RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs. 47 <test>
48 <param name="input" value="rnaz_input_trna.aln"/>
49 <output name="outfile" file="rnaz_result_trna.fasta"/>
50 </test>
51 <test>
52 <param name="input" value="rnaz_test_input2.aln"/>
53 <output name="outfile" file="rnaz_result2.fasta"/>
54 </test>
55 </tests>
56 <help>
57 <![CDATA[
58
59 **What it does**
60
61 RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs.
62
63 **Input**
64
65 Input is a multiple sequence alignment file. Currently the the following alignment formats can be read: CLUSTALW, FASTA, PHYLIP,NEXUS, MAF, and XMFA. Alignments can be generated by any sequence based alignment program. Sequence alignment tools can be found in Galaxy too (e.g. ClustalW).
66
67 Example:
68
69 CLUSTAL 2.1 multiple sequence alignment
43 70
44 71
45 Gruber AR, Findeiss, Washietl S, Hofacker IL, and Stadler PF. 72 sacCer1 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
46 RNAz 2.0: Improved noncoding rna detection. 73
47 Pac Symp Biocomput, 2010. 15:69–79. 74 sacKlu GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC
75
76 sacBay GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
77
78 sacCas GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC
79
80 \** * * \** \** \**\** \** \**\** * *\** \**\**\* *\**\* * \**\**\** *
81
82
83 **Output**
84
85 In Galaxy RNAz gives you 2 output files: a summary file and a result file. For the example input they look like this:
86
87 Summary:
88
89 Sequences: 4
90 Columns: 60
91 Reading direction: forward
92 Mean pairwise identity: 82.50
93 Shannon entropy: 0.28395
94 G+C content: 0.51667
95 Mean single sequence MFE: -16.67
96 Consensus MFE: -15.59
97 Energy contribution: -15.53
98 Covariance contribution: -0.06
99 Combinations/Pair: 1.26
100 Mean z-score: -0.66
101 Structure conservation index: 0.93
102 Background model: mononucleotide
103 Decision model: sequence based alignment quality
104 SVM decision value: -0.64
105 SVM RNA-class probability: 0.238023
106 Prediction: OTHER
107
108
109 Result file:
110
111 >sacCer1
112
113 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC
114
115 ..((((...((((........))))....(((((((((((....))))))))))))))). ( -19.00, z-score = -1.44, R)
116
117 >sacKlu
118
119 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGC
120
121 ..((((...((((........))))....((((((((..(....)..)))))))))))). ( -16.00, z-score = -0.11, R)
122
123 >sacBay
124
125 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC
126
127 ..((((...((((........))))....(((((((((((....))))))))))))))). ( -19.00, z-score = -1.44, R)
128
129 >sacCas
130
131 GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAAC
132
133 .((((((..((((........))))..............)))))).(((......))).. ( -12.69, z-score = 0.35, R)
134
135 >consensus
136
137 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC
138
139 ..((((...((((........))))....(((((((((((....))))))))))))))). (-15.59 = -15.53 + -0.06)
140
141
142
143
144
145
146 ]]>
147
48 </help> 148 </help>
149
150 <citations>
151 <citation type="doi">10.1142/9789814295291_0009</citation>
152 </citations>
153
49 </tool> 154 </tool>