Mercurial > repos > iuc > hmmer_hmmbuild

comparison jackhmmer.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_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy1">
4 <description>iteratively search a protein sequence against a protein database (PSIBLAST-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_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@">
14 <description>iteratively search a protein sequence against a protein database (PSIBLAST-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 jackhmmer
24 -N $N
25 @OFORMAT_WITH_OPTS@
26 @HSSI@
27 @THRESHOLDS@
28 @ACCEL_HEUR@
29 @ARSWS@
30 @AEEWS@
31 @PRIOR@
32
33 @EVAL_CALIB@
34 @ADV_OPTS@
35 @CPU@
36 @SEED@
37
38 '$seqfile'
39 '$seqdb'
40 > '$output'
41 ]]></command>
42 <inputs>
43 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
44 <!-- todo use Galaxy features like data libraries/data tables/??? -->
45 <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
46 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
47 <expand macro="oformat_with_opts_dom"/>
48 <expand macro="hssi"/>
49 <expand macro="thresholds_xml"/>
50 <expand macro="accel_heur_xml"/>
51 <expand macro="arsws"/>
52 <expand macro="aeews"/>
53 <expand macro="prior"/>
54 <expand macro="eval_calib_xml"/>
55 <expand macro="adv_opts"/>
56 <expand macro="seed"/>
57 </inputs>
58 <outputs>
59 <expand macro="output_dom_pfam" tool="JACKHMMER"/>
60 </outputs>
61 <tests>
62 <test expect_num_outputs="3">
63 <param name="seqfile" value="uniprot_matches.fasta"/>
64 <param name="seqdb" value="globins45.fa"/>
65 <expand macro="oformat_test" />
66 <expand macro="seed_test" />
67 <output name="output" file="jackhmmer.out" lines_diff="180">
68 <expand macro="assert_out" tool="jackhmmer"/>
69 </output>
70 <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10">
71 <expand macro="assert_tblout" tool="jackhmmer"/>
72 </output>
73 <output name="tblout" file="jackhmmer.tblout" lines_diff="10">
74 <expand macro="assert_tblout" tool="jackhmmer"/>
75 </output>
76 </test>
77 <test expect_num_outputs="1">
78 <param name="seqfile" value="uniprot_matches.fasta"/>
79 <param name="seqdb" value="globins45.fa"/>
80 <expand macro="oformat_test" />
81 <param name="oformat" value=""/>
82 <expand macro="seed_test" />
83 <output name="output" file="jackhmmer.out" lines_diff="180">
84 <expand macro="assert_out" tool="jackhmmer"/>
85 </output>
86 </test>
87 </tests>
88 <help><![CDATA[
89 @HELP_PRE@
90
91 jackhmmer iteratively searches each query sequence in <seqfile> against the
92 target sequence(s) in <seqdb>. The first iteration is identical to a phmmer
93 search. For the next iteration, a multiple alignment of the query together
94 with all target sequences satisfying inclusion thresholds is assembled, a
95 profile is constructed from this alignment (identical to using hmmbuild on the
96 alignment), and profile search of the <seqdb> is done (identical to an
97 hmmsearch with the profile).
98
99
100 @HELP_PRE_OTH@
101
102 @OFORMAT_WITH_OPTS_HELP_NOPFAM@
103 @HSSI_HELP@
104 @THRESHOLDS_HELP@
105 @ACCEL_HEUR_HELP@
106 @ARSWS_HELP@
107 @AEEWS_HELP@
108 @PRIOR_HELP@
109 @EVAL_CALIB_HELP@
110 @ADV_OPTS_HELP@
111 @SEED_HELP@
112
113 @ATTRIBUTION@
114 ]]></help>
115 <expand macro="citation"/>
116 </tool>