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comparison rnalien.xml @ 0:7df5f5a32031 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien commit 5385435d8f4339d609f69076cc755e0dc2e7bc72
author rnateam
date Tue, 07 Mar 2017 13:15:20 -0500
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1 <tool id="RNAlien" name="RNAlien" version="1.3.5">
2 <description>
3 Unsupervised covariance model construction from a single input sequence
4 </description>
5 <requirements>
6 <requirement type="package" version="1.3.5">rnalien</requirement>
7 </requirements>
8 <command detect_errors="aggressive"><![CDATA[
9 RNAlien
10 -i '$input_sequence'
11 #if $t
12 -t $t
13 #end if
14 -o `pwd`
15 -d outdir
16 -c "\${GALAXY_SLOTS:-4}"
17 -z $z
18 -e $e
19 -b $blast_database
20 $s
21 $f
22 $a
23 > 'warnings'
24 ]]>
25 </command>
26 <inputs>
27 <param name="input_sequence" type="data" format="fasta" label="Input sequence"/>
28 <param argument="-t" type="integer" value=""
29 label="NCBI taxonomy id of input organism" optional="true" help="-t"/>
30 <param argument="-z" type="float" value="1.0" min="0.1"
31 label="Only candidate sequences with a nSCI higher than this value are accepted." help=""/>
32 <param argument="-e" type="float" value="0.001" min="0.000000000001"
33 label="Evalue cutoff for cmsearch filtering" help=""/>
34 <param name="blast_database" type="select" label="Specify name of blast database to use."
35 help="Blast databases, e.g. nt, refseq_genomic,..">
36 <option value="nt">nt</option>
37 <option value="refseq_genomic">refseq_genomic</option>
38 <option value="refseq_rna">refseq_rna</option>
39 <option value="refseq_representative_genomes">refseq_representative_genomes</option>
40 </param>
41 <param argument="-a" truevalue="-a" falsevalue="" checked="True" type="boolean"
42 label="Filter blast hits by coverage of at least 80%." help=""/>
43 <param argument="-s" truevalue="-s" falsevalue="" checked="False" type="boolean"
44 label="Only the best blast hit per taxonomic entry is considered." help=""/>
45 <param argument="-f" truevalue="-f" falsevalue="" checked="True" type="boolean"
46 label="Toggles blast softmasking, meaning exclusion of low complexity (repetative) regions in lookup table." help=""/>
47 </inputs>
48 <outputs>
49 <data format="txt" name="log" from_work_dir="./outdir/Log" label="RNAlien construction summary"/>
50 <data format="cm" name="cm" from_work_dir="./outdir/result.cm" label="RNAlien result covariance model"/>
51 <data format="stockholm" name="stockholm" from_work_dir="./outdir/result.stockholm" label="RNAlien result stockholm alignment"/>
52 <data format="fasta" name="sequences" from_work_dir="./outdir/result.fa" label="RNAlien result sequences"/>
53 <data format="txt" name="warnings" from_work_dir="warnings" label="Warnings from tool dependencies"/>
54 </outputs>
55 <tests>
56 <test>
57 <param name="input_sequence" value="tcvh4.fa"/>
58 <param name="taxonomy_id" value="10239"/>
59 <output name="warnings" file="warnings"/>
60 </test>
61 </tests>
62 <help>
63
64 <![CDATA[
65
66 **What it does**
67
68 RNAlien is a tool for automatic construction of RNAfamily models from a single sequence.
69
70 **Input**
71
72 Example:
73
74 >AJ243001.2
75
76 ATACTTACCTGGCACAGGGGATACCACGATCACCAAGGTGGTTCCCCCAAGACGAGGCTC
77
78 ACCATTGCACTCCGGTGGCGCTGACCCTTGCAATGACCCCAAATGTGGGTTACTCGGGTG
79
80 TGTAATTTCTGTTAGCTGGGGACTGCGTTCGCGCTTTCCCCTT
81
82 **Options**
83 -i Path to input fasta file
84 -o Path to output directory
85 -t NCBI taxonomy ID number of input RNA organism
86 -z Only candidate sequences with a nSCI higher than this value are accepted. 1.0
87 -e Evalue cutoff for cmsearch filtering. 0.001
88 -b Specify name of blast database to use. nt
89 -a Filter blast hits by coverage of at least 80%. True
90 -s Only the best blast hit per taxonomic entry is considered. False
91 -f Toggles blast softmasking, meaning exclusion of low complexity (repetative) regions in lookup table. True
92 -r Restrict search space to taxonomic kingdom (bacteria,archea,eukaryia).
93
94 **Output**
95
96 RNAlien collects potential family members in multiple iterations.
97
98 The output of RNAlien consists of a stockholm alignment, a covariance
99
100 model and a Log file.
101
102 For further questions please refer to the RNAlien Help page.
103
104 .. _Userguide: http://nibiru.tbi.univie.ac.at/rnalien/help _.
105
106 ]]>
107
108 </help>
109 <citations>
110 <citation type="doi">10.1093/nar/gkw558</citation>
111 </citations>
112 </tool>