Mercurial > repos > bgruening > rnaz
comparison rnaz.xml @ 2:580ee1e91801 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e85474d72b07c70ca061f51b7165951038a06a6c
author | bgruening |
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date | Thu, 28 Sep 2017 11:21:09 -0400 |
parents | e23c455f8335 |
children | 58fd61a8362e |
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1:e23c455f8335 | 2:580ee1e91801 |
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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" /> |