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comparison hmmscan.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_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.0">
3 <description>search sequence(s) against a profile database</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 ## "Press" database
11 hmmpress $hmmfile;
12 ## Scan
13 hmmscan
14
15 @OFORMAT_WITH_OPTS@
16 @THRESHOLDS@
17 @CUT@
18 @ACCEL_HEUR@
19 @ADV_OPTS@
20 @CPU@
21 @SEED@
22
23 $hmmfile
24 $seqfile
25 > $output;
26 ## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype
27 rm ${hmmfile}.h3m ${hmmfile}.h3i ${hmmfile}.h3f ${hmmfile}.h3p;
28 ]]></command>
29 <inputs>
30 <expand macro="input_hmm" />
31 <!-- todo use Galaxy features like data libraries/data tables/??? -->
32 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
33 <expand macro="oformat_with_opts"/>
34 <expand macro="thresholds_xml"/>
35 <expand macro="cut"/>
36 <expand macro="accel_heur_xml"/>
37 <expand macro="adv_opts"/>
38 <expand macro="seed"/>
39 </inputs>
40 <outputs>
41 <data format="txt" name="output" label="HMM matches of $seqfile.name in $hmmfile.name"/>
42 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
43 <filter>'tblout' in oformat</filter>
44 </data>
45 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
46 <filter>'domtblout' in oformat</filter>
47 </data>
48 <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
49 <filter>'pfamtblout' in oformat</filter>
50 </data>
51 </outputs>
52 <tests>
53 <test>
54 <param name="hmmfile" value="MADE1.hmm"/>
55 <param name="seqfile" value="dna_target.fa"/>
56 <expand macro="oformat_test" />
57 <expand macro="seed_test" />
58 <output name="output" file="MADE1.out" lines_diff="20"/>
59 <output name="tblout" file="MADE1.out.tblout" lines_diff="20"/>
60 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="20"/>
61 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="20"/>
62 </test>
63 </tests>
64 <help><![CDATA[
65 @HELP_PRE@
66
67 hmmscan is used to search protein sequences against collections of protein
68 profiles. For each sequence in <seqfile>, use that query sequence to search the
69 target database of profiles in <hmmfile>, and output ranked lists of the profiles
70 with the most significant matches to the sequence.
71
72 @HELP_PRE_OTH@
73
74 @OFORMAT_WITH_OPTS_HELP@
75 @THRESHOLDS_HELP@
76 @CUT_HELP@
77 @ACCEL_HEUR_HELP@
78 @ADV_OPTS_HELP@
79 @SEED_HELP@
80
81 @ATTRIBUTION@
82 ]]></help>
83 <expand macro="citation"/>
84 </tool>