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comparison jackhmmer.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_jackhmmer" name="jackhmmer" version="@WRAPPER_VERSION@.0">
3 <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 jackhmmer
11 -N $N
12 @OFORMAT_WITH_OPTS_NOPFAM@
13 @HSSI@
14 @THRESHOLDS@
15 @ACCEL_HEUR@
16 @MCSS@
17 @ARSWS@
18 @AEEWS@
19 @PRIOR@
20
21 @EVAL_CALIB@
22 @ADV_OPTS@
23 @CPU@
24 @SEED@
25
26 $seqfile
27 $seqdb
28 > $output
29 ]]></command>
30 <inputs>
31 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
32 <!-- todo use Galaxy features like data libraries/data tables/??? -->
33 <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
34 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
35 <expand macro="oformat_with_opts_nopfam"/>
36 <expand macro="hssi"/>
37 <expand macro="thresholds_xml"/>
38 <expand macro="accel_heur_xml"/>
39 <expand macro="mcss"/>
40 <expand macro="arsws"/>
41 <expand macro="aeews"/>
42 <expand macro="prior"/>
43 <expand macro="eval_calib_xml"/>
44 <expand macro="adv_opts"/>
45 <expand macro="seed"/>
46 </inputs>
47 <outputs>
48 <data format="txt" name="output" label="PHMMER search of $seqfile.name in $seqdb.name"/>
49 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
50 <filter>'tblout' in str(oformat)</filter>
51 </data>
52 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
53 <filter>'domtblout' in str(oformat)</filter>
54 </data>
55 </outputs>
56 <tests>
57 <test>
58 <param name="seqfile" value="uniprot_matches.fasta"/>
59 <param name="seqdb" value="globins45.fa"/>
60 <expand macro="oformat_test" />
61 <expand macro="seed_test" />
62 <output name="output" file="jackhmmer.out" lines_diff="180"/>
63 <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10"/>
64 <output name="tblout" file="jackhmmer.tblout" lines_diff="10"/>
65 </test>
66 </tests>
67 <help><![CDATA[
68 @HELP_PRE@
69
70 jackhmmer iteratively searches each query sequence in <seqfile> against the
71 target sequence(s) in <seqdb>. The first iteration is identical to a phmmer
72 search. For the next iteration, a multiple alignment of the query together
73 with all target sequences satisfying inclusion thresholds is assembled, a
74 profile is constructed from this alignment (identical to using hmmbuild on the
75 alignment), and profile search of the <seqdb> is done (identical to an
76 hmmsearch with the profile).
77
78
79 @HELP_PRE_OTH@
80
81 @OFORMAT_WITH_OPTS_HELP_NOPFAM@
82 @HSSI_HELP@
83 @THRESHOLDS_HELP@
84 @ACCEL_HEUR_HELP@
85 @MCSS_HELP@
86 @ARSWS_HELP@
87 @AEEWS_HELP@
88 @PRIOR_HELP@
89 @EVAL_CALIB_HELP@
90 @ADV_OPTS_HELP@
91 @SEED_HELP@
92
93 @ATTRIBUTION@
94 ]]></help>
95 <expand macro="citation"/>
96 </tool>