Mercurial > repos > iuc > hmmer_hmmbuild

comparison nhmmer.xml.orig @ 10:51970d0e7bd7 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:40:07 +0000
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9:5c83ba4417e6 10:51970d0e7bd7
1 <?xml version="1.0"?>
2 <<<<<<< HEAD
3 <tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@+galaxy1">
4 <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <expand macro="stdio"/>
10 <command><![CDATA[
11 @ADDTHREADS@
12 =======
13 <tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@">
14 <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
15 <expand macro="bio_tools"/>
16 <macros>
17 <import>macros.xml</import>
18 </macros>
19 <expand macro="requirements"/>
20 <expand macro="stdio"/>
21 <command><![CDATA[
22 >>>>>>> c37d72558 (add more bio.tool IDs)
23 nhmmer
24
25 @OFORMAT_WITH_OPTS@
26 @HSSI@
27 @THRESHOLDS_NODOM@
28 @CUT@
29 @ACCEL_HEUR@
30 @FORMAT_SELECTOR@
31 @ADV_OPTS@
32 @LENGTHS@
33 @CPU@
34 @SEED@
35
36 '$hmmfile'
37 '$seqfile'
38 > '$output'
39 ]]></command>
40 <inputs>
41 <expand macro="input_hmm" />
42 <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
43 <expand macro="oformat_with_opts_dfam_alisc"/>
44 <expand macro="hssi"/>
45 <expand macro="thresholds_nodom"/>
46 <expand macro="cut" />
47 <expand macro="accel_heur_xml"/>
48 <expand macro="format_selector_noprot"/>
49 <expand macro="adv_opts"/>
50 <expand macro="lengths"/>
51 <!-- TODO: block_length toponly bottomonly -->
52 <expand macro="seed"/>
53 </inputs>
54 <outputs>
55 <expand macro="output_dfam_alisc" tool="NHMMER"/>
56 </outputs>
57 <tests>
58 <test expect_num_outputs="4">
59 <param name="hmmfile" value="MADE1.hmm"/>
60 <param name="seqfile" value="dna_target.fa"/>
61 <expand macro="oformat_test" />
62 <param name="oformat" value="tblout,dfamtblout,aliscoresout"/>
63 <expand macro="seed_test" />
64 <output name="output" file="nhmmer.out" lines_diff="16">
65 <expand macro="assert_out" tool="nhmmer"/>
66 </output>
67 <output name="tblout" file="nhmmer.out.tblout" lines_diff="12">
68 <expand macro="assert_tblout" tool="nhmmer"/>
69 </output>
70 <output name="aliscoresout" file="nhmmer.out.aliscoresout" lines_diff="10"/>
71 <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10">
72 <assert_contents>
73 <has_line_matching expression="# hit scores"/>
74 </assert_contents>
75 </output>
76 </test>
77 <test expect_num_outputs="1">
78 <param name="hmmfile" value="MADE1.hmm"/>
79 <param name="seqfile" value="dna_target.fa"/>
80 <expand macro="oformat_test" />
81 <param name="oformat" value=""/>
82 <expand macro="seed_test" />
83 <output name="output" file="nhmmer.out" lines_diff="16">
84 <expand macro="assert_out" tool="nhmmer"/>
85 </output>
86 </test>
87 </tests>
88 <help><![CDATA[
89 @HELP_PRE@
90
91 nhmmer is used to search one or more nucleotide queries against a nucleotide
92 sequence database. For each query in <queryfile>, use that query to search the
93 target database of sequences in <seqdb>, and output a ranked list of the hits
94 with the most significant matches to the query. A query may be either a profile
95 model built using hmmbuild, a sequence alignment, or a single sequence.
96 Sequence based queries can be in a number of formats (see --qformat), and can
97 typically be autodetected. Note that only Stockholm format supports the use of
98 multiple sequence-based queries.
99
100 @HELP_PRE_OTH@
101
102 @OFORMAT_WITH_OPTS_N_HELP@
103 @HSSI_HELP@
104 @THRESHOLDS_NODOM_HELP@
105 @CUT_HELP@
106 @ACCEL_HEUR_HELP@
107 @FORMAT_SELECTOR_HELP@
108 @ADV_OPTS_HELP@
109 @LENGTHS_HELP@
110 @SEED_HELP@
111
112 @ATTRIBUTION@
113 ]]></help>
114 <expand macro="citation"/>
115 </tool>