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comparison hmmsearch.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_hmmsearch" name="hmmsearch" version="@WRAPPER_VERSION@.0">
3 <description>search profile(s) against a sequence database</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 hmmsearch
11
12 @OFORMAT_WITH_OPTS@
13 @THRESHOLDS@
14 @CUT@
15 @ACCEL_HEUR@
16 @ADV_OPTS@
17 @CPU@
18 @SEED@
19
20 $hmmfile
21 $seqdb
22 > $output
23 ]]></command>
24 <inputs>
25 <expand macro="input_hmm" />
26 <!-- todo use Galaxy features like data libraries/data tables/??? -->
27 <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/>
28 <expand macro="oformat_with_opts"/>
29 <expand macro="thresholds_xml"/>
30 <expand macro="cut"/>
31 <expand macro="accel_heur_xml"/>
32 <expand macro="adv_opts"/>
33 <expand macro="seed"/>
34 </inputs>
35 <outputs>
36 <data format="txt" name="output" label="HMM matches of $hmmfile.name in $seqdb.name"/>
37 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $hmmfile.name in $seqdb.name">
38 <filter>'tblout' in str(oformat)</filter>
39 </data>
40 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $hmmfile.name in $seqdb.name">
41 <filter>'domtblout' in str(oformat)</filter>
42 </data>
43 <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $hmmfile.name in $seqdb.name">
44 <filter>'pfamtblout' in str(oformat)</filter>
45 </data>
46 </outputs>
47 <tests>
48 <test>
49 <param name="hmmfile" value="globins4.hmm"/>
50 <param name="seqdb" value="uniprot_matches.fasta"/>
51 <expand macro="oformat_test" />
52 <expand macro="seed_test" />
53 <output name="output" file="uniprot_globins_match.out" lines_diff="20"/>
54 <output name="domtblout" file="globins.domtblout" lines_diff="10"/>
55 <output name="pfamtblout" file="globins.pfamtblout" lines_diff="10"/>
56 <output name="tblout" file="globins.tblout" lines_diff="10"/>
57 </test>
58 </tests>
59 <help><![CDATA[
60 @HELP_PRE@
61
62 hmmsearch is used to search one or more profiles against a sequence database.
63 For each profile in <hmmfile>, use that query profile to search the target
64 database of sequences in <seqdb>, and output ranked lists of the sequences with
65 the most significant matches to the profile. To build profiles from multiple
66 alignments, see hmmbuild.
67
68 @HELP_PRE_OTH@
69
70 @OFORMAT_WITH_OPTS_HELP@
71 @THRESHOLDS_HELP@
72 @CUT_HELP@
73 @ACCEL_HEUR_HELP@
74 @ADV_OPTS_HELP@
75 @SEED_HELP@
76
77 @ATTRIBUTION@
78 ]]></help>
79 <expand macro="citation"/>
80 </tool>