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comparison rnaalifold.xml @ 4:0def54ac03a6 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
author rnateam
date Tue, 18 Jul 2017 01:52:38 -0400
parents 40b99ecd575f
children
comparison
equal deleted inserted replaced
3:e7ae00c71743 4:0def54ac03a6
1 <tool id="viennarna_rnaalifold" name="@EXECUTABLE@" version="@VERSION@.0"> 1 <tool id="viennarna_rnaalifold" name="@EXECUTABLE@" version="@VERSION@.1">
2 <description>Calculate minimum free energy secondary structures and partition function on a multiple alignment file</description> 2 <description>Calculate minimum free energy secondary structures and partition function on a multiple alignment file</description>
3 <macros> 3 <macros>
4 <token name="@EXECUTABLE@">RNAalifold</token> 4 <token name="@EXECUTABLE@">RNAalifold</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 12
13 RNAalifold < '$input' > '$tabularFile' 13 RNAalifold < '$input' > '$tabularFile'
14
15 #if $input.ext == 'clustal':
16 -f C
17 #else if $input.ext == 'fasta':
18 -f F
19 #else if $input.ext == 'stockholm':
20 -f S
21 #else if $input.ext == 'maf':
22 -f M
23 #else:
24 -f C
25 #end if
14 -T$model_options.temperature -d$model_options.dangling 26 -T$model_options.temperature -d$model_options.dangling
15 $general_options.verbose 27 $general_options.verbose
16 $general_options.color 28 $general_options.color
17 $general_options.alignment 29 $general_options.alignment
18 #if $general_options.layout_type ==0 30 #if $general_options.layout_type ==0
48 #if $constraints.shapeOption.m <> 1.8 or $constraints.shapeOption.b <> -0.6 60 #if $constraints.shapeOption.m <> 1.8 or $constraints.shapeOption.b <> -0.6
49 #set $s="Dm"+str($constraints.shapeOption.m)+"b"+str($constraints.shapeOption.b) 61 #set $s="Dm"+str($constraints.shapeOption.m)+"b"+str($constraints.shapeOption.b)
50 --shapeMethod=$s 62 --shapeMethod=$s
51 #end if 63 #end if
52 #end if 64 #end if
53 #end if 65 #end if
66
54 #if $algorithm_options.pf <> "-1" 67 #if $algorithm_options.pf <> "-1"
55 --partfunc=$algorithm_options.pf 68 --partfunc=$algorithm_options.pf
56 #end if 69 --pfScale=$algorithm_options.pfScale
57 #if $algorithm_options.mea <> 1.0 70
58 --mea=$algorithm_options.mea 71 #end if
59 #end if 72 #if $algorithm_options.measelect.mea == "yes":
73 --MEA=$algorithm_options.measelect.meavalue
74 --pfScale=$algorithm_options.pfScale
75 #end if
76
60 $algorithm_options.mis 77 $algorithm_options.mis
61 #if $algorithm_options.stochBT_en <> 1 78 #if $algorithm_options.stochBT_en <> 1
62 --stochBT_en=$algorithm_options.stochBT_en 79 --stochBT_en=$algorithm_options.stochBT_en
63 #end if
64 #if $algorithm_options.pfScale <> 1.07
65 --pfScale=$algorithm_options.pfScale
66 #end if 80 #end if
67 $algorithm_options.circular 81 $algorithm_options.circular
68 #if $algorithm_options.bppmThreshold <> 1e-6 82 #if $algorithm_options.bppmThreshold <> 1e-6
69 --bppmThreshold=$algorithm_options.bppmThreshold 83 --bppmThreshold=$algorithm_options.bppmThreshold
70 #end if 84 #end if
90 #end if 104 #end if
91 && tar -cf '$imagesFile' *.ps 105 && tar -cf '$imagesFile' *.ps
92 ]]> 106 ]]>
93 </command> 107 </command>
94 <inputs> 108 <inputs>
95 <param format="txt" name="input" type="data" label="Clustal file"/> 109 <param format="clustal,fasta,stockholm,maf" name="input" type="data" label="Clustal/AlignmentFasta/Stockholm/MAF file"/>
110
96 <section name="algorithm_options" title="Algorithm Options"> 111 <section name="algorithm_options" title="Algorithm Options">
97 <param name="pf" type="select" label="Calculate partition function" help="Calculate the partition function and base pairing probability matrix in addition to the mfe structure. Default is calculation of mfe structure only." argument="-p"> 112 <param name="pf" type="select" label="Calculate partition function" help="Calculate the partition function and base pairing probability matrix in addition to the mfe structure. Default is calculation of mfe structure only." argument="-p">
98 <option value="-1" selected="true">None</option> 113 <option value="-1" selected="true">None</option>
99 <option value="0">0: Deactivates the calculation of the pair probabilities, saving about 50% in runtime</option> 114 <option value="0">0: Deactivates the calculation of the pair probabilities, saving about 50% in runtime</option>
100 <option value="1" >1: Calculate the partition function and base pairing probability matrix</option> 115 <option value="1" >1: Calculate the partition function and base pairing probability matrix</option>
101 </param> 116 </param>
102 <param name="mea" type="float" value="1.0" label="Gamma Value" help="Calculate an MEA (maximum expected accuracy) structure. The parameter gamma tunes the importance of correctly predicted pairs versus unpaired bases. Thus, for small values of gamma the MEA structure will contain only pairs with very high probability. where the expected accuracy is computed from the pair probabilities: each base pair (i,j) gets a score 2*gamma*p_ij and the score of an unpaired base is given by the probability of not forming a pair." argument="--MEA"/> 117
118 <conditional name="measelect">
119 <param name="mea" type="select" label="Calculate Maximum Expected accuracy" argument="--MEA">
120 <option value="no">No</option>
121 <option value="yes">Yes</option>
122 </param>
123 <when value="yes">
124 <param name="meavalue" type="float" value="1.0" label="Gamma Value" help="Calculate an MEA (maximum expected accuracy) structure. The parameter gamma tunes the importance of correctly predicted pairs versus unpaired bases. Thus, for small values of gamma the MEA structure will contain only pairs with very high probability. where the expected accuracy is computed from the pair probabilities: each base pair (i,j) gets a score 2*gamma*p_ij and the score of an unpaired base is given by the probability of not forming a pair."/>
125 </when>
126 </conditional>
127
103 <param argument="--mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="Output 'most informative sequence' instead of simple consensu"/> 128 <param argument="--mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="Output 'most informative sequence' instead of simple consensu"/>
104 <param name="stochBT_en" type="integer" value="1" label="Number of random structures." help="Compute a certain number of random structures with a probability dependend on the partition function. Print out the energies and probabilities of the backtraced structures. " argument="--stochBT_en"/> 129 <param name="stochBT_en" type="integer" value="1" label="Number of random structures." help="Compute a certain number of random structures with a probability dependend on the partition function. Print out the energies and probabilities of the backtraced structures. " argument="--stochBT_en"/>
105 <param name="pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences." argument="--pfScale"/> 130 <param name="pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences." argument="--pfScale"/>
106 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/> 131 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
107 <param name="bppmThreshold" type="float" value="1e-6" label="Threshold for base pair probabilities" help="By setting the threshold the base pair probabilities that are included in the output can be varied. By default only those exceeding 1e−5 in probability will be shown as squares in the dot plot. Changing the threshold to any other value allows for increase or decrease of data." argument="--bppmThreshold"/> 132 <param name="bppmThreshold" type="float" value="1e-6" label="Threshold for base pair probabilities" help="By setting the threshold the base pair probabilities that are included in the output can be varied. By default only those exceeding 1e−5 in probability will be shown as squares in the dot plot. Changing the threshold to any other value allows for increase or decrease of data." argument="--bppmThreshold"/>
215 <tests> 240 <tests>
216 <test> 241 <test>
217 <param name="input" value="rnaalifold_input1.clustal"/> 242 <param name="input" value="rnaalifold_input1.clustal"/>
218 <output name="output" file="rnaalifold_result1.txt"/> 243 <output name="output" file="rnaalifold_result1.txt"/>
219 </test> 244 </test>
245 <test>
246 <param name="input" value="rnaalifold_input1.fa"/>
247 <output name="output" file="rnaalifold_resultfa.txt"/>
248 </test>
249 <test>
250 <param name="input" value="rnaalifold_input1.stk"/>
251 <output name="output" file="rnaalifold_resultstk.txt"/>
252 </test>
253 <test>
254 <param name="input" value="rnaalifold_input1.clustal"/>
255 <param name="mea" value="yes"/>
256 <output name="output" file="rnaalifold_result_MEA.txt"/>
257 </test>
258
259
220 </tests> 260 </tests>
221 <help> 261 <help>
222 <![CDATA[ 262 <![CDATA[
223 **RNAalifold** 263 **RNAalifold**
224 264
225 ----- 265 -----
226 266
227 **Input format** 267 **Input format**
228 268
229 RNAalifold requires one input file 269 RNAalifold requires one input file
230 - Clustal file 270 - Clustal/AlignmentFasta/Stockholm/MAF file
231 271
232 ------ 272 ------
233 273
234 **Outputs** 274 **Outputs**
235 275