Mercurial > repos > iuc > hmmer_nhmmer
comparison nhmmer.xml @ 3:c8e81e43bff1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author | iuc |
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date | Sat, 07 Apr 2018 03:50:51 -0400 |
parents | ae4754e7c97a |
children | b4fe2f703b4b |
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2:ae4754e7c97a | 3:c8e81e43bff1 |
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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> |