Mercurial > repos > rnateam > intarna

comparison intarna.xml @ 6:3f6715821198 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit da73dae857c2ee9447aad05f260f7da5ea1db3a6
author rnateam
date Tue, 10 Apr 2018 12:24:44 -0400
parents 233dfabc8592
children fd067a1143f3
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5:233dfabc8592 6:3f6715821198
1 <tool id="intarna" name="IntaRNA" version="2.1.0.2"> 1 <tool id="intarna" name="IntaRNA" version="2.2.0">
2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description> 2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
3 <macros> 3 <macros>
4 <macro name="query_macro"> 4 <macro name="query_macro">
5 <param name="_query" argument="--query" format="fasta" type="data" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" /> 5 <param name="_query" argument="--query" format="fasta" type="data" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" />
6 <conditional name="qAcc_cond"> 6 <conditional name="qAcc_cond">
46 label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/> 46 label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
47 <param argument="--tAccL" type="integer" value="100" min="0" max="99999" 47 <param argument="--tAccL" type="integer" value="100" min="0" max="99999"
48 label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'tAccW'"/> 48 label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'tAccW'"/>
49 </macro> 49 </macro>
50 <macro name="seed_macro"> 50 <macro name="seed_macro">
51 <param argument="--noSeed" truevalue="--noSeed" falsevalue="" checked="False" type="boolean" 51 <param argument="--noSeed" truevalue="--noSeed" falsevalue="" checked="false" type="boolean"
52 label="Disable seed constraint entirely for computation" help=""/> 52 label="Disable seed constraint entirely for computation" help=""/>
53 <param argument="--seedBP" type="integer" value="7" min="2" max="20" label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/> 53 <param argument="--seedBP" type="integer" value="7" min="2" max="20" label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/>
54 <param argument="--seedMaxUP" type="integer" value="0" min="0" max="20" 54 <param argument="--seedMaxUP" type="integer" value="0" min="0" max="20"
55 label="Max. overall number of unpaired bases (query+target)" help=""/> 55 label="Max. overall number of unpaired bases (query+target)" help=""/>
56 </macro> 56 </macro>
82 <option value="B">in both sequences</option> 82 <option value="B">in both sequences</option>
83 </param> 83 </param>
84 </macro> 84 </macro>
85 </macros> 85 </macros>
86 <requirements> 86 <requirements>
87 <requirement type="package" version="2.1.0">intarna</requirement> 87 <requirement type="package" version="2.2.0">intarna</requirement>
88 </requirements> 88 </requirements>
89 <stdio> 89 <stdio>
90 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 90 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
91 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 91 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
92 </stdio> 92 </stdio>