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comparison rnaz.xml @ 2:580ee1e91801 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e85474d72b07c70ca061f51b7165951038a06a6c
author bgruening
date Thu, 28 Sep 2017 11:21:09 -0400
parents e23c455f8335
children 58fd61a8362e
comparison
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1:e23c455f8335 2:580ee1e91801
1 <tool id="rnaz" name="RNAz" version="2.1.0"> 1 <tool id="rnaz" name="RNAz" version="2.1.1">
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 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>
13 <version_command>RNAz --version</version_command> 13 <version_command>RNAz --version</version_command>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 RNAz '$input' 16 RNAz '$input'
17 --$forward_or_reverse 17 --$forward_or_reverse
18 $dinucleotide 18 $zscore
19 $mononucleotide
20 $locarnate 19 $locarnate
21 $noshuffle 20 $noshuffle
22 #if $cutoff != -1.0: 21 #if $cutoff != -1.0:
23 --cutoff=$cutoff 22 --cutoff=$cutoff
24 #end if 23 #end if
32 <param name="forward_or_reverse" type="select" label="Scored strand"> 31 <param name="forward_or_reverse" type="select" label="Scored strand">
33 <option value="forward">Score forward strand (-f)</option> 32 <option value="forward">Score forward strand (-f)</option>
34 <option value="reverse">Score reverse strand (-r)</option> 33 <option value="reverse">Score reverse strand (-r)</option>
35 <option value="both-strands">Score both strands (-b)</option> 34 <option value="both-strands">Score both strands (-b)</option>
36 </param> 35 </param>
36 <param name="zscore" type="select" label="Which type of z-scores">
37 <option value="--mononucleotide">Use mononucleotide shuffled z-scores</option>
38 <option value="--dinucleotide" selected="true">Use dinucleotide shuffled z-scores</option>
39 </param>
37 <param argument="--cutoff" label="Probability cutoff" type="float" value="-1.0" help="-1.0 to deactivate"/> 40 <param argument="--cutoff" label="Probability cutoff" type="float" value="-1.0" help="-1.0 to deactivate"/>
38 <param argument="--dinucleotide" type="boolean" checked="true" truevalue="--dinucleotide" falsevalue="" label="Use dinucleotide shuffled z-scores" />
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="--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" /> 42 <param argument="--no-shuffle" name="noshuffle" type="boolean" checked="false" truevalue="--no-shuffle" falsevalue="" label="Never fall back to shuffling" />
42 </inputs> 43 </inputs>
43 <outputs> 44 <outputs>
44 <data name="outfile" format="fasta" /> 45 <data name="outfile" format="fasta" />