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comparison rnazSelectSeqs.xml @ 0:273a961d332f draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
author bgruening
date Wed, 30 Jan 2019 04:13:47 -0500
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1 <tool id="rnaz_select_seqs" name="RNAz Select Seqs" version="2.1">
2 <requirements>
3 <requirement type="package" version="2.1">rnaz</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 rnazSelectSeqs.pl
7 --num-seqs $numseqs
8 --num-samples $numsamples
9 --opt-id $optid
10 --max-id $maxid
11 #if $noref:
12 --no-ref $noref
13 #end if
14 '$input'
15 > '$output'
16 ]]></command>
17 <inputs>
18 <param format="txt" name="input" type="data" label="Input Alignment File" />
19 <param argument="--num-seqs" name="numseqs" type="integer" value="6" label="Number of sequences in the output alignment(s). (Default:6)" />
20 <param argument="--num-samples" name="numsamples" type="integer" value="1" label="Number of output alignments (Default: 1)" />
21 <param argument="--opt-id" name="optid" type="integer" value="80"
22 label="The resulting alignment(s) is (are) optimized for this value of mean pairwise identity (in percent, default: 80)" />
23 <param argument="--max-id" name="maxid" type="integer" value="99"
24 label="Sequences from pairs with pairwise identity higher than X% are removed (default: 99, i.e. only almost identical sequences areremoved)" />
25 <param argument="--no-reference" name="noref" type="boolean" checked="false" truevalue="--no-reference" falsevalue=""
26 label="By default the first sequence (=reference sequence) is always present in the output alignment(s). If you do not care having it removed, set this flag." />
27 </inputs>
28 <outputs>
29 <data name="output" format="txt" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="input" value="tRNA.aln"/>
34 <param name="numseqs" value="1"/>
35 <output name="output" file="tRNA_selected.aln"/>
36 </test>
37 </tests>
38 <help><![CDATA[ RNAz up to version 1.0 was limited to alignments
39 of at most 6 sequences. As of version 2.0, there is no limit on
40 the maximum number of sequences. However, under some cirumstances
41 (e.g. for very large alignments) it is still useful to reduce the
42 number of sequences prior to running RNAz. You can select an
43 optimal subset of sequences using rnazSelectSeqs.pl before you
44 put it into RNAz:
45
46 Usage:
47 rnazSelectSeqs.pl [options] [file]
48
49 Options:
50 -n N, --num-seqs=N
51 Number of sequences in the output alignment(s). (Default:6)
52
53 -a N, --num-samples=N
54 Number of output alignments (Default: 1)
55
56 -i X, --opt-id=X
57 The resulting alignment(s) is (are) optimized for this value of
58 mean pairwise identity (in percent, default: 80)
59
60 --max-id=X
61 Sequences from pairs with pairwise identity higher than X% are
62 removed (default: 99, i.e. only almost identical sequences are
63 removed)
64
65 -x, --no-reference
66 By default the first sequence (=reference sequence) is always
67 present in the output alignment(s). If you do not care having it
68 removed, set this flag.
69
70 -v, --version
71 Prints version information and exits.
72
73 -h, --help
74 Prints a short help message and exits.
75
76 --man Prints a detailed manual page and exits.
77
78
79 ]]></help>
80
81 <citations>
82 <citation type="doi">10.1142/9789814295291_0009</citation>
83 </citations>
84
85 </tool>