Mercurial > repos > iuc > hmmer_hmmbuild

comparison hmmscan.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_hmmscan" name="hmmscan" version="@TOOL_VERSION@+galaxy1">
4 <description>search protein sequence(s) against a protein profile database</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_hmmscan" name="hmmscan" version="@TOOL_VERSION@">
14 <description>search protein sequence(s) against a protein profile database</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 @INPUTHMMCHOICE@
24 hmmscan
25
26 @OFORMAT_WITH_OPTS@
27 @THRESHOLDS@
28 @CUT@
29 @ACCEL_HEUR@
30 @ADV_OPTS@
31 @CPU@
32 @SEED@
33
34 '$input_hmm_filename'
35 '$seqfile'
36 > '$output'
37 ]]></command>
38 <inputs>
39 <expand macro="input_hmm_choice" />
40 <!-- todo use Galaxy features like data libraries/data tables/??? -->
41 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
42 <expand macro="oformat_with_opts_dom_pfam"/>
43 <expand macro="thresholds_xml"/>
44 <expand macro="cut"/>
45 <expand macro="accel_heur_xml"/>
46 <expand macro="adv_opts"/>
47 <expand macro="seed"/>
48 </inputs>
49 <outputs>
50 <expand macro="output_dom_pfam" tool="HMMSCAN"/>
51 </outputs>
52 <tests>
53 <test expect_num_outputs="4">
54 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
55 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
56 <param name="seqfile" value="dna_target.fa"/>
57 <expand macro="oformat_test" />
58 <expand macro="seed_test" />
59 <output name="output" file="MADE1.out" lines_diff="24">
60 <expand macro="assert_out" tool="hmmscan"/>
61 </output>
62 <output name="tblout" file="MADE1.out.tblout" lines_diff="14">
63 <expand macro="assert_tblout" tool="hmmscan"/>
64 </output>
65 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="10">
66 <expand macro="assert_tblout" tool="hmmscan"/>
67 </output>
68 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="10">
69 <expand macro="assert_tblout" tool="hmmscan"/>
70 </output>
71 </test>
72 </tests>
73 <help><![CDATA[
74 @HELP_PRE@
75
76 hmmscan is used to search protein sequences against collections of protein
77 profiles. For each sequence in <seqfile>, use that query sequence to search the
78 target database of profiles in <hmmfile>, and output ranked lists of the profiles
79 with the most significant matches to the sequence.
80
81 @HELP_PRE_OTH@
82
83 @OFORMAT_WITH_OPTS_HELP@
84 @THRESHOLDS_HELP@
85 @CUT_HELP@
86 @ACCEL_HEUR_HELP@
87 @ADV_OPTS_HELP@
88 @SEED_HELP@
89
90 @ATTRIBUTION@
91 ]]></help>
92 <expand macro="citation"/>
93 </tool>