Mercurial > repos > bgruening > rnaz_select_seqs

annotate rnazSelectSeqs.xml @ 0:5f31010cdd15 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 03:58:28 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
1 <tool id="rnaz_select_seqs" name="RNAz Select Seqs" version="2.1">
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
2 <requirements>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
3 <requirement type="package" version="2.1">rnaz</requirement>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
4 </requirements>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
6 rnazSelectSeqs.pl
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
7 --num-seqs $numseqs
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
8 --num-samples $numsamples
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
9 --opt-id $optid
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
10 --max-id $maxid
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
11 #if $noref:
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
12 --no-ref $noref
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
13 #end if
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
14 '$input'
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
15 > '$output'
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
16 ]]></command>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
17 <inputs>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
18 <param format="txt" name="input" type="data" label="Input Alignment File" />
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
19 <param argument="--num-seqs" name="numseqs" type="integer" value="6" label="Number of sequences in the output alignment(s). (Default:6)" />
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
20 <param argument="--num-samples" name="numsamples" type="integer" value="1" label="Number of output alignments (Default: 1)" />
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
21 <param argument="--opt-id" name="optid" type="integer" value="80"
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
22 label="The resulting alignment(s) is (are) optimized for this value of mean pairwise identity (in percent, default: 80)" />
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
23 <param argument="--max-id" name="maxid" type="integer" value="99"
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
24 label="Sequences from pairs with pairwise identity higher than X% are removed (default: 99, i.e. only almost identical sequences areremoved)" />
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
25 <param argument="--no-reference" name="noref" type="boolean" checked="false" truevalue="--no-reference" falsevalue=""
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
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." />
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
27 </inputs>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
28 <outputs>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
29 <data name="output" format="txt" />
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
30 </outputs>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
31 <tests>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
32 <test>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
33 <param name="input" value="tRNA.aln"/>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
34 <param name="numseqs" value="1"/>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
35 <output name="output" file="tRNA_selected.aln"/>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
36 </test>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
37 </tests>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
38 <help><![CDATA[ RNAz up to version 1.0 was limited to alignments
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
39 of at most 6 sequences. As of version 2.0, there is no limit on
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
40 the maximum number of sequences. However, under some cirumstances
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
41 (e.g. for very large alignments) it is still useful to reduce the
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
42 number of sequences prior to running RNAz. You can select an
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
43 optimal subset of sequences using rnazSelectSeqs.pl before you
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
44 put it into RNAz:
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
45
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
46 Usage:
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
47 rnazSelectSeqs.pl [options] [file]
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
48
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
49 Options:
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
50 -n N, --num-seqs=N
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
51 Number of sequences in the output alignment(s). (Default:6)
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
52
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
53 -a N, --num-samples=N
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
54 Number of output alignments (Default: 1)
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
55
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
56 -i X, --opt-id=X
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
57 The resulting alignment(s) is (are) optimized for this value of
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
58 mean pairwise identity (in percent, default: 80)
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
59
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
60 --max-id=X
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
61 Sequences from pairs with pairwise identity higher than X% are
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
62 removed (default: 99, i.e. only almost identical sequences are
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
63 removed)
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
64
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
65 -x, --no-reference
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
66 By default the first sequence (=reference sequence) is always
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
67 present in the output alignment(s). If you do not care having it
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
68 removed, set this flag.
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
69
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
70 -v, --version
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
71 Prints version information and exits.
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
72
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
73 -h, --help
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
74 Prints a short help message and exits.
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
75
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
76 --man Prints a detailed manual page and exits.
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
77
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
78
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
79 ]]></help>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
80
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
81 <citations>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
82 <citation type="doi">10.1142/9789814295291_0009</citation>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
83 </citations>
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
84
5f31010cdd15 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
85 </tool>