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comparison intarna.xml @ 13:ddfd02440cfa draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 76e8f82fd859dcb91b5704df4fd5d2d154ad799e"
author bgruening
date Tue, 12 Apr 2022 15:47:18 +0000
parents 0a2817800fd9
children d3db19200b24
comparison
equal deleted inserted replaced
12:0a2817800fd9 13:ddfd02440cfa
1 <tool id="intarna" name="IntaRNA" version="3.2.0"> 1 <tool id="intarna" name="IntaRNA" version="3.3.1">
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 argument="--query" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Query sequence(s)" name="query" type="data" /> 5 <param argument="--query" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Query sequence(s)" name="query" type="data" />
6 <conditional name="qAcc_cond"> 6 <conditional name="qAcc_cond">
62 <option value="N">in none of the sequences</option> 62 <option value="N">in none of the sequences</option>
63 <option value="T">in the target only</option> 63 <option value="T">in the target only</option>
64 <option selected="true" value="Q">in the query only</option> 64 <option selected="true" value="Q">in the query only</option>
65 <option value="B">in both sequences</option> 65 <option value="B">in both sequences</option>
66 </param> 66 </param>
67 <param argument="--outPairwise" checked="false" falsevalue="" help="" label="Enables pairwise sequence processing, i.e. interactions are only computed for each corresponding query-target pair (same index) instead of all-vs-all" truevalue="--outPairwise" type="boolean" />
67 </macro> 68 </macro>
68 </macros> 69 </macros>
69 <requirements> 70 <requirements>
70 <requirement type="package" version="3.2.0">intarna</requirement> 71 <requirement type="package" version="3.3.1">intarna</requirement>
71 </requirements> 72 </requirements>
72 <version_command>IntaRNA --version</version_command> 73 <version_command>IntaRNA --version</version_command>
73 <command detect_errors="exit_code"><![CDATA[ 74 <command detect_errors="exit_code"><![CDATA[
74 75
75 IntaRNA 76 IntaRNA
110 --outSep "`printf "\t"`" 111 --outSep "`printf "\t"`"
111 --outNumber $advancedOptions.output.outNumber 112 --outNumber $advancedOptions.output.outNumber
112 --outOverlap $advancedOptions.output.outOverlap 113 --outOverlap $advancedOptions.output.outOverlap
113 --outCsvCols '$advancedOptions.output.outCsvCols' 114 --outCsvCols '$advancedOptions.output.outCsvCols'
114 --outCsvSort '$advancedOptions.output.outCsvSort' 115 --outCsvSort '$advancedOptions.output.outCsvSort'
116 $advancedOptions.output.outPairwise
115 #if $advancedOptions.advancedSelector == "advanced" 117 #if $advancedOptions.advancedSelector == "advanced"
116 ## Query parameters 118 ## Query parameters
117 --qIntLoopMax $advancedOptions.query.qIntLoopMax 119 --qIntLoopMax $advancedOptions.query.qIntLoopMax
118 #if $advancedOptions.query.qRegion 120 #if $advancedOptions.query.qRegion
119 --qRegion '$advancedOptions.query.qRegion' 121 --qRegion '$advancedOptions.query.qRegion'