Mercurial > repos > iuc > hmmer_nhmmscan
comparison nhmmscan.xml @ 8:fb1305d0d1c6 draft default tip
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"/> |