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comparison hmmalign.xml @ 0:62479bdcc059 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
author iuc
date Tue, 12 May 2015 15:04:26 -0400
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-1:000000000000 0:62479bdcc059
1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmalign" name="hmmalign" version="@WRAPPER_VERSION@.0">
3 <description>align sequences to a profile HMM</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 hmmalign
11
12 $trim
13 @FORMAT_SELECTOR@
14 --outformat stockholm
15
16 $hmmfile
17 $seq
18 > $output
19 ]]></command>
20 <inputs>
21 <param name="seq" type="data" format="fasta" label="Sequence to align against model" help="Sequence should be in FASTA format"/>
22 <expand macro="input_hmm" />
23 <!-- TODO: mapali -->
24 <param name="trim" type="boolean" truevalue="--trim" label="trim terminal tails of nonaligned residues from alignment" help="(--trim)" falsevalue=""/>
25 <expand macro="format_selector"/>
26 </inputs>
27 <outputs>
28 <data format="stockholm" name="output" label="Alignment of $seq.name to $hmmfile.name">
29 </data>
30 </outputs>
31 <tests>
32 <test>
33 <param name="hmmfile" value="globins4.hmm"/>
34 <param name="seq" value="globins45.fa"/>
35 <output name="output" file="globins-45-align.sto" lines_diff="20"/>
36 </test>
37 </tests>
38 <help><![CDATA[
39 @HELP_PRE@
40
41 Perform a multiple sequence alignment of all the sequences in <seqfile> by
42 aligning them individually to the profile HMM in <hmmfile>. The new alignment
43 is output to stdout in Stockholm format. The <hmmfile> should contain only a
44 single profile. If it contains more, only the first profile in the file will be
45 used.
46
47 Either <hmmfile> or <seqfile> (but not both) may be ’-’ (dash), which means
48 reading this input from stdin rather than a file.
49
50 The sequences in <seqfile> are aligned in unihit local alignment mode.
51 Therefore they should already be known to contain only a single domain (or a
52 fragment of one). The optimal alignment may assign some residues as
53 nonhomologous (N and C states), in which case these residues are still included
54 in the resulting alignment, but shoved to the outer edges. To trim these
55 unaligned nonhomologous residues from the result, see the --trim option.
56
57
58 @HELP_PRE_OTH@
59
60 @FORMAT_SELECTOR_HELP@
61
62 @ATTRIBUTION@
63 ]]></help>
64 <expand macro="citation"/>
65 </tool>