Mercurial > repos > iuc > hmmer_hmmsearch

comparison hmmsearch.xml @ 8:3bb58751f4ee draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 061757dd7b3bfe66b7738fd54bd6c5e135d9afe8
author iuc
date Mon, 06 Nov 2023 20:22:49 +0000
parents d753d9169482
children df7a52791be9
comparison
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7:d753d9169482 8:3bb58751f4ee
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy0"> 2 <tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy1">
3 <description>search profile(s) against a sequence database</description> 3 <description>search profile(s) against a sequence database</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <expand macro="stdio"/> 9 <expand macro="stdio"/>
9 <command><![CDATA[ 10 <command><![CDATA[
10 @ADDTHREADS@ 11 @ADDTHREADS@
11 hmmsearch 12 hmmsearch
12 13
13 @OFORMAT_WITH_OPTS@ 14 @OFORMAT_WITH_OPTS@
14 @THRESHOLDS@ 15 @THRESHOLDS@
15 @CUT@ 16 @THRESHOLDS_DOM@
16 @ACCEL_HEUR@ 17 @ACCEL_HEUR@
17 @ADV_OPTS@ 18 @ADV_OPTS@
18 @CPU@ 19 @CPU@
19 @SEED@ 20 @SEED@
20 21
25 <inputs> 26 <inputs>
26 <expand macro="input_hmm" /> 27 <expand macro="input_hmm" />
27 <!-- todo use Galaxy features like data libraries/data tables/??? --> 28 <!-- todo use Galaxy features like data libraries/data tables/??? -->
28 <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/> 29 <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/>
29 <expand macro="oformat_with_opts_dom_pfam"/> 30 <expand macro="oformat_with_opts_dom_pfam"/>
30 <expand macro="thresholds_xml"/> 31 <expand macro="thresholds_cut_dom_xml"/>
31 <expand macro="cut"/>
32 <expand macro="accel_heur_xml"/> 32 <expand macro="accel_heur_xml"/>
33 <expand macro="adv_opts"/> 33 <expand macro="adv_opts"/>
34 <expand macro="seed"/> 34 <expand macro="seed"/>
35 </inputs> 35 </inputs>
36 <outputs> 36 <outputs>
63 <expand macro="seed_test" /> 63 <expand macro="seed_test" />
64 <output name="output" file="uniprot_globins_match.out" lines_diff="20"> 64 <output name="output" file="uniprot_globins_match.out" lines_diff="20">
65 <expand macro="assert_out" tool="hmmsearch"/> 65 <expand macro="assert_out" tool="hmmsearch"/>
66 </output> 66 </output>
67 </test> 67 </test>
68 <test expect_num_outputs="1"><!-- test with additional evalue threshold options set -->
69 <param name="hmmfile" value="fn3.hmm"/>
70 <param name="seqdb" value="uniprot_matches.fasta"/>
71 <conditional name="repopt">
72 <param name="incE" value="0.00001"/>
73 <param name="incdomE" value="0.0001"/>
74 </conditional>
75 <expand macro="oformat_test" />
76 <param name="oformat" value=""/>
77 <expand macro="seed_test" />
78 <output name="output">
79 <expand macro="assert_out" tool="hmmsearch"/>
80 </output>
81 <assert_command>
82 <has_text text="-E 10"/>
83 <has_text text="--incE 1e-05"/>
84 <has_text text="--domE 10"/>
85 <has_text text="--incdomE 0.0001"/>
86 </assert_command>
87 </test>
88 <test expect_num_outputs="1"><!-- test with cut_ga set -->
89 <param name="hmmfile" value="fn3.hmm"/>
90 <param name="seqdb" value="uniprot_matches.fasta"/>
91 <conditional name="repopt">
92 <param name="repopt_sel" value="--cut_ga"/>
93 </conditional>
94 <expand macro="oformat_test" />
95 <param name="oformat" value=""/>
96 <expand macro="seed_test" />
97 <output name="output" file="cut_ga_test.out" lines_diff="10">
98 <expand macro="assert_out" tool="hmmsearch"/>
99 </output>
100 </test>
101
102
68 </tests> 103 </tests>
69 <help><![CDATA[ 104 <help><![CDATA[
70 @HELP_PRE@ 105 @HELP_PRE@
71 106
72 hmmsearch is used to search one or more profiles against a sequence database. 107 hmmsearch is used to search one or more profiles against a sequence database.