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comparison hmmsearch.xml @ 9:df7a52791be9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 721504306833ba97c91f285e5bfd86efc04875ee
author iuc
date Sun, 25 Feb 2024 18:31:05 +0000
parents 3bb58751f4ee
children
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8:3bb58751f4ee 9:df7a52791be9
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy1"> 2 <tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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="bio_tools"/>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <expand macro="stdio"/> 9 <command detect_errors="aggressive"><![CDATA[
10 <command><![CDATA[
11 @ADDTHREADS@ 10 @ADDTHREADS@
12 hmmsearch 11 hmmsearch
13 12
14 @OFORMAT_WITH_OPTS@ 13 @OFORMAT_WITH_OPTS@
15 @THRESHOLDS@ 14 @THRESHOLDS@
40 <test expect_num_outputs="4"> 39 <test expect_num_outputs="4">
41 <param name="hmmfile" value="globins4.hmm"/> 40 <param name="hmmfile" value="globins4.hmm"/>
42 <param name="seqdb" value="uniprot_matches.fasta"/> 41 <param name="seqdb" value="uniprot_matches.fasta"/>
43 <expand macro="oformat_test" /> 42 <expand macro="oformat_test" />
44 <expand macro="seed_test" /> 43 <expand macro="seed_test" />
45 <output name="output" file="uniprot_globins_match.out" lines_diff="20"> 44 <output name="output" file="uniprot_globins_match.out" lines_diff="24">
46 <expand macro="assert_out" tool="hmmsearch"/> 45 <expand macro="assert_out" tool="hmmsearch"/>
47 </output> 46 </output>
48 <output name="domtblout" file="globins.domtblout" lines_diff="16"> 47 <output name="domtblout" file="globins.domtblout" lines_diff="16">
49 <expand macro="assert_tblout" tool="hmmsearch"/> 48 <expand macro="assert_tblout" tool="hmmsearch"/>
50 </output> 49 </output>
92 <param name="repopt_sel" value="--cut_ga"/> 91 <param name="repopt_sel" value="--cut_ga"/>
93 </conditional> 92 </conditional>
94 <expand macro="oformat_test" /> 93 <expand macro="oformat_test" />
95 <param name="oformat" value=""/> 94 <param name="oformat" value=""/>
96 <expand macro="seed_test" /> 95 <expand macro="seed_test" />
97 <output name="output" file="cut_ga_test.out" lines_diff="10"> 96 <output name="output" file="cut_ga_test.out" lines_diff="14">
98 <expand macro="assert_out" tool="hmmsearch"/> 97 <expand macro="assert_out" tool="hmmsearch"/>
99 </output> 98 </output>
100 </test> 99 </test>
101
102
103 </tests> 100 </tests>
104 <help><![CDATA[ 101 <help><![CDATA[
105 @HELP_PRE@ 102 @HELP_PRE@
106 103
107 hmmsearch is used to search one or more profiles against a sequence database. 104 hmmsearch is used to search one or more profiles against a sequence database.