Mercurial > repos > iuc > hmmer_nhmmscan

comparison nhmmscan.xml @ 8:fb1305d0d1c6 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 18:32:37 +0000
parents e7d281a290a6
children
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7:e7d281a290a6 8:fb1305d0d1c6
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@+galaxy1"> 2 <tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>search DNA sequence(s) against a DNA profile database</description> 3 <description>search DNA sequence(s) against a DNA profile 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 @INPUTHMMCHOICE@ 11 @INPUTHMMCHOICE@
13 nhmmscan 12 nhmmscan
14 13
15 @OFORMAT_WITH_OPTS@ 14 @OFORMAT_WITH_OPTS@
52 <param name="input_hmm_conditional|input_hmm_source" value="history"/> 51 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
53 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/> 52 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
54 <param name="seqfile" value="dna_target.fa"/> 53 <param name="seqfile" value="dna_target.fa"/>
55 <expand macro="oformat_test" /> 54 <expand macro="oformat_test" />
56 <expand macro="seed_test" /> 55 <expand macro="seed_test" />
57 <output name="output" file="MADE1.nhmmscan_out" lines_diff="12"> 56 <output name="output" file="MADE1.nhmmscan_out" lines_diff="18">
58 <expand macro="assert_out" tool="nhmmscan"/> 57 <expand macro="assert_out" tool="nhmmscan"/>
59 </output> 58 </output>
60 <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10"> 59 <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10">
61 <!-- nhmmscan reports as hmmscan https://github.com/EddyRivasLab/hmmer/issues/190 --> 60 <!-- nhmmscan reports as hmmscan https://github.com/EddyRivasLab/hmmer/issues/190 -->
62 <expand macro="assert_tblout" tool="nhmmscan"/> 61 <expand macro="assert_tblout" tool="nhmmscan"/>