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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty
author rnateam
date Sat, 11 Mar 2017 16:59:55 -0500
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1 <tool id="selectsequencesfrommsa" name="Select Sequences" version="1.0.2">
2 <description>
3 Tool to select representative sequences from a multiple sequence alignment.
4 </description>
5 <requirements>
6 <requirement type="package" version="1.0.2">selectsequencesfrommsa</requirement>
7 </requirements>
8 <command detect_errors="aggressive"><![CDATA[
9 SelectSequencesFromMSA
10 -c '$input_clustal'
11 $x
12 -o `pwd`
13 -n $n
14 -i $i
15 -m $m
16 > warnings
17 ]]>
18 </command>
19 <inputs>
20 <param name="input_clustal" type="data" format="clustal" label="Input clustal alignment"/>
21 <param argument="-n" type="integer" value="6" min="1" label="Number of sequences in the output alignment." help=""/>
22 <param argument="-i" type="float" value="80" min="0.1" label="Optimize for this percentage of mean pairwise identity" help=""/>
23 <param argument="-m" type="float" value="95" min="0.1" label="Sequences with a higher percentage of pairwise identity will be removed." help=""/>
24 <param argument="-x" truevalue="-x" falsevalue="" checked="True" type="boolean" label="The first sequence (=reference sequence) is always present in the output alignment." help=""/>
25 </inputs>
26 <outputs>
27 <data format="clustal" name="clustal" from_work_dir="result.selected" label="Clustal alignment of selected sequences"/>
28 </outputs>
29 <tests>
30 <test>
31 <param name="input_clustal" value="result.clustal"/>
32 <output name="result.selected" file="result.selected"/>
33 </test>
34 </tests>
35 <help>
36
37 <![CDATA[
38
39 **What it does**
40
41 Tool to select representative sequences from a multiple sequence alignment in clustal format.
42 Useful before running RNAz, RNAcode, RNAalifold on alignments with many entries.
43
44 **Input**
45 Multiple sequence alignment in clustal format
46
47 **Options**
48 -n Number of sequences in the output alignment. (Default: 6)
49 -i Optimize for this percentage of mean pairwise identity (Default: 80)
50 -m Sequences with a higher percentage of pairwise identity will be removed (Default: 95)
51 -x The first sequence (=reference sequence) is always present in the output alignment per default. Default: True
52
53 **Output**
54 Clustal alignment with selected sequences
55
56 ]]>
57
58 </help>
59 <citations>
60 <citation type="doi">10.1093/nar/gkw558</citation>
61 </citations>
62 </tool>