Mercurial > repos > iuc > hmmer_nhmmer

comparison nhmmer.xml @ 3:c8e81e43bff1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:50:51 -0400
parents ae4754e7c97a
children b4fe2f703b4b
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2:ae4754e7c97a 3:c8e81e43bff1
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_nhmmer" name="nhmmer" version="@WRAPPER_VERSION@.0"> 2 <tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@">
3 <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description> 3 <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
18 @ADV_OPTS@ 18 @ADV_OPTS@
19 @LENGTHS@ 19 @LENGTHS@
20 @CPU@ 20 @CPU@
21 @SEED@ 21 @SEED@
22 22
23 $hmmfile 23 '$hmmfile'
24 $seqfile 24 '$seqfile'
25 > $output 25 > '$output'
26 ]]></command> 26 ]]></command>
27 <inputs> 27 <inputs>
28 <expand macro="input_hmm" /> 28 <expand macro="input_hmm" />
29 <param name="seqfile" type="data" format="fasta" label="Target sequence file"/> 29 <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
30 <expand macro="oformat_with_opts_n"/> 30 <expand macro="oformat_with_opts_n"/>
31 <expand macro="hssi"/> 31 <expand macro="hssi"/>
55 <test> 55 <test>
56 <param name="hmmfile" value="MADE1.hmm"/> 56 <param name="hmmfile" value="MADE1.hmm"/>
57 <param name="seqfile" value="dna_target.fa"/> 57 <param name="seqfile" value="dna_target.fa"/>
58 <expand macro="oformat_test" /> 58 <expand macro="oformat_test" />
59 <expand macro="seed_test" /> 59 <expand macro="seed_test" />
60 <output name="output" file="nhmmer.out" lines_diff="32"/> 60 <output name="output" file="nhmmer.out" lines_diff="10" />
61 <output name="tblout" file="nhmmer.out.tblout" lines_diff="10" />
62 <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10" />
61 </test> 63 </test>
62 </tests> 64 </tests>
63 <help><![CDATA[ 65 <help><![CDATA[
64 @HELP_PRE@ 66 @HELP_PRE@
65 67
83 @ADV_OPTS_HELP@ 85 @ADV_OPTS_HELP@
84 @LENGTHS_HELP@ 86 @LENGTHS_HELP@
85 @SEED_HELP@ 87 @SEED_HELP@
86 88
87 @ATTRIBUTION@ 89 @ATTRIBUTION@
88 ]]></help> 90 ]]></help>
89 <expand macro="citation"/> 91 <expand macro="citation"/>
90 </tool> 92 </tool>