annotate jackhmmer.xml @ 5:5113c71c7031 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author iuc
date Tue, 16 Jun 2020 05:32:33 -0400
parents 793967b6ae8a
children d9ce554da9b4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
3
036df14999e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 2
diff changeset
2 <tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@">
0
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
3 <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
4 <macros>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
5 <import>macros.xml</import>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
6 </macros>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
8 <expand macro="stdio"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
9 <command><![CDATA[
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
10 jackhmmer
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
11 -N $N
5
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
12 @OFORMAT_WITH_OPTS@
0
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
13 @HSSI@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
14 @THRESHOLDS@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
15 @ACCEL_HEUR@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
16 @ARSWS@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
17 @AEEWS@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
18 @PRIOR@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
19
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
20 @EVAL_CALIB@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
21 @ADV_OPTS@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
22 @CPU@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
23 @SEED@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
24
3
036df14999e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 2
diff changeset
25 '$seqfile'
036df14999e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 2
diff changeset
26 '$seqdb'
036df14999e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 2
diff changeset
27 > '$output'
036df14999e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 2
diff changeset
28 ]]></command>
0
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
29 <inputs>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
30 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
31 <!-- todo use Galaxy features like data libraries/data tables/??? -->
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
32 <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
33 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
5
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
34 <expand macro="oformat_with_opts_dom"/>
0
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
35 <expand macro="hssi"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
36 <expand macro="thresholds_xml"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
37 <expand macro="accel_heur_xml"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
38 <expand macro="arsws"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
39 <expand macro="aeews"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
40 <expand macro="prior"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
41 <expand macro="eval_calib_xml"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
42 <expand macro="adv_opts"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
43 <expand macro="seed"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
44 </inputs>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
45 <outputs>
5
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
46 <expand macro="output_dom_pfam" tool="JACKHMMER"/>
0
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
47 </outputs>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
48 <tests>
5
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
49 <test expect_num_outputs="3">
0
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
50 <param name="seqfile" value="uniprot_matches.fasta"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
51 <param name="seqdb" value="globins45.fa"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
52 <expand macro="oformat_test" />
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
53 <expand macro="seed_test" />
5
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
54 <output name="output" file="jackhmmer.out" lines_diff="180">
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
55 <expand macro="assert_out" tool="jackhmmer"/>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
56 </output>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
57 <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10">
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
58 <expand macro="assert_tblout" tool="jackhmmer"/>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
59 </output>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
60 <output name="tblout" file="jackhmmer.tblout" lines_diff="10">
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
61 <expand macro="assert_tblout" tool="jackhmmer"/>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
62 </output>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
63 </test>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
64 <test expect_num_outputs="1">
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
65 <param name="seqfile" value="uniprot_matches.fasta"/>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
66 <param name="seqdb" value="globins45.fa"/>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
67 <expand macro="oformat_test" />
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
68 <param name="oformat" value=""/>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
69 <expand macro="seed_test" />
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
70 <output name="output" file="jackhmmer.out" lines_diff="180">
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
71 <expand macro="assert_out" tool="jackhmmer"/>
5113c71c7031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 4
diff changeset
72 </output>
0
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
73 </test>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
74 </tests>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
75 <help><![CDATA[
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
76 @HELP_PRE@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
77
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
78 jackhmmer iteratively searches each query sequence in <seqfile> against the
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
79 target sequence(s) in <seqdb>. The first iteration is identical to a phmmer
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
80 search. For the next iteration, a multiple alignment of the query together
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
81 with all target sequences satisfying inclusion thresholds is assembled, a
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
82 profile is constructed from this alignment (identical to using hmmbuild on the
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
83 alignment), and profile search of the <seqdb> is done (identical to an
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
84 hmmsearch with the profile).
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
85
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
86
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
87 @HELP_PRE_OTH@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
88
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
89 @OFORMAT_WITH_OPTS_HELP_NOPFAM@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
90 @HSSI_HELP@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
91 @THRESHOLDS_HELP@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
92 @ACCEL_HEUR_HELP@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
93 @ARSWS_HELP@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
94 @AEEWS_HELP@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
95 @PRIOR_HELP@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
96 @EVAL_CALIB_HELP@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
97 @ADV_OPTS_HELP@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
98 @SEED_HELP@
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
99
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
100 @ATTRIBUTION@
3
036df14999e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 2
diff changeset
101 ]]></help>
0
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
102 <expand macro="citation"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
103 </tool>