Mercurial > repos > iuc > hmmer3

comparison nhmmer.xml @ 0:62479bdcc059 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:62479bdcc059
1 <?xml version="1.0"?>
2 <tool id="hmmer_nhmmer" name="nhmmer" version="@WRAPPER_VERSION@.0">
3 <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 nhmmer
11
12 @OFORMAT_WITH_OPTS_N@
13 @HSSI@
14 @THRESHOLDS_NODOM@
15 @CUT@
16 @ACCEL_HEUR@
17 @FORMAT_SELECTOR@
18 @ADV_OPTS@
19 @LENGTHS@
20 @CPU@
21 @SEED@
22
23 $hmmfile
24 $seqfile
25 > $output
26 ]]></command>
27 <inputs>
28 <expand macro="input_hmm" />
29 <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
30 <expand macro="oformat_with_opts_n"/>
31 <expand macro="hssi"/>
32 <expand macro="thresholds_nodom"/>
33 <expand macro="cut" />
34 <expand macro="accel_heur_xml"/>
35 <expand macro="format_selector_noprot"/>
36 <expand macro="adv_opts"/>
37 <expand macro="lengths"/>
38 <!-- TODO: block_length toponly bottomonly -->
39 <expand macro="seed"/>
40 </inputs>
41 <outputs>
42 <data format="txt" name="output" label="NHMMER search of $seqfile.name in $hmmfile.name"/>
43
44 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
45 <filter>'tblout' in str(oformat)</filter>
46 </data>
47 <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
48 <filter>'pfamtblout' in str(oformat)</filter>
49 </data>
50 <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name">
51 <filter>'aliscoresout' in str(oformat)</filter>
52 </data>
53 </outputs>
54 <tests>
55 <test>
56 <param name="hmmfile" value="MADE1.hmm"/>
57 <param name="seqfile" value="dna_target.fa"/>
58 <expand macro="oformat_test" />
59 <expand macro="seed_test" />
60 <output name="output" file="nhmmer.out" lines_diff="32"/>
61 </test>
62 </tests>
63 <help><![CDATA[
64 @HELP_PRE@
65
66 nhmmer is used to search one or more nucleotide queries against a nucleotide
67 sequence database. For each query in <queryfile>, use that query to search the
68 target database of sequences in <seqdb>, and output a ranked list of the hits
69 with the most significant matches to the query. A query may be either a profile
70 model built using hmmbuild, a sequence alignment, or a single sequence.
71 Sequence based queries can be in a number of formats (see --qformat), and can
72 typically be autodetected. Note that only Stockholm format supports the use of
73 multiple sequence-based queries.
74
75 @HELP_PRE_OTH@
76
77 @OFORMAT_WITH_OPTS_N_HELP@
78 @HSSI_HELP@
79 @THRESHOLDS_NODOM_HELP@
80 @CUT_HELP@
81 @ACCEL_HEUR_HELP@
82 @FORMAT_SELECTOR_HELP@
83 @ADV_OPTS_HELP@
84 @LENGTHS_HELP@
85 @SEED_HELP@
86
87 @ATTRIBUTION@
88 ]]></help>
89 <expand macro="citation"/>
90 </tool>