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comparison nhmmscan.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_nhmmscan" name="nhmmscan" version="@WRAPPER_VERSION@.0">
3 <description>search DNA sequence(s) against a DNA profile database</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 hmmpress $hmmfile;
11
12 nhmmscan
13
14 @OFORMAT_WITH_OPTS_N@
15 @THRESHOLDS_NODOM@
16 @CUT@
17 @ACCEL_HEUR@
18 --B1 $B1
19 --B2 $B2
20 --B3 $B3
21
22 @ADV_OPTS@
23 @LENGTHS@
24 @CPU@
25 @SEED@
26
27 $hmmfile
28 $seqfile
29 > $output
30 ]]></command>
31 <inputs>
32 <expand macro="input_hmm" />
33 <!-- todo use Galaxy features like data libraries/data tables/??? -->
34 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
35 <expand macro="oformat_with_opts_n"/>
36 <expand macro="thresholds_nodom"/>
37 <expand macro="cut"/>
38 <expand macro="accel_heur_xml"/>
39
40 <param name="B1" type="integer" label="window length for biased-composition modifier (MSV)" help="(--B1)" value="110"/>
41 <param name="B2" type="integer" label="window length for biased-composition modifier (Vit)" help="(--B2)" value="240"/>
42 <param name="B3" type="integer" label="window length for biased-composition modifier (Fwd)" help="(--B3)" value="1000"/>
43
44 <expand macro="adv_opts"/>
45 <expand macro="lengths"/>
46 <expand macro="seed"/>
47 </inputs>
48 <outputs>
49 <data format="txt" name="output" label="HMM matches of $seqfile.name in $hmmfile.name"/>
50
51 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
52 <filter>'tblout' in str(oformat)</filter>
53 </data>
54 <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
55 <filter>'pfamtblout' in str(oformat)</filter>
56 </data>
57 <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name">
58 <filter>'aliscoresout' in str(oformat)</filter>
59 </data>
60 </outputs>
61 <tests>
62 <test>
63 <param name="hmmfile" value="MADE1.hmm"/>
64 <param name="seqfile" value="dna_target.fa"/>
65 <expand macro="oformat_test" />
66 <expand macro="seed_test" />
67 <output name="output" file="MADE1.out" lines_diff="120"/>
68 <output name="tblout" file="MADE1.out.tblout" lines_diff="30"/>
69 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="30"/>
70 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="36"/>
71 </test>
72 </tests>
73 <help><![CDATA[
74 @HELP_PRE@
75
76 nhmmscan is used to search nucleotide sequences against collections of
77 nucleotide profiles. For each sequence in <seqfile>, use that query sequence to
78 search the target database of profiles in <hmmfile>, and output ranked lists of
79 the profiles with the most significant matches to the sequence.
80
81 The <seqfile> may contain more than one query sequence. It can be in FASTA
82 format, or several other common sequence file formats (genbank, embl, and
83 uniprot, among others), or in alignment file formats (stockholm, aligned fasta,
84 and others). See the --qformat option for a complete list.
85
86 @HELP_PRE_OTH@
87
88 @OFORMAT_WITH_OPTS_N_HELP@
89 @THRESHOLDS_NODOM_HELP@
90 @CUT_HELP@
91 @ACCEL_HEUR_HELP@
92 @BIAS_COMP_HELP@
93 @ADV_OPTS_HELP@
94 @LENGTHS_HELP@
95 @SEED_HELP@
96
97
98 @ATTRIBUTION@
99 ]]></help>
100 <expand macro="citation"/>
101 </tool>