Mercurial > repos > iuc > hmmer_hmmsearch
comparison hmmsearch.xml @ 5:b774ae8e1609 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author | iuc |
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date | Tue, 16 Jun 2020 05:27:07 -0400 |
parents | 6867ed975e25 |
children | 192a5046d9a2 |
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4:6867ed975e25 | 5:b774ae8e1609 |
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23 ]]></command> | 23 ]]></command> |
24 <inputs> | 24 <inputs> |
25 <expand macro="input_hmm" /> | 25 <expand macro="input_hmm" /> |
26 <!-- todo use Galaxy features like data libraries/data tables/??? --> | 26 <!-- todo use Galaxy features like data libraries/data tables/??? --> |
27 <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/> | 27 <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/> |
28 <expand macro="oformat_with_opts"/> | 28 <expand macro="oformat_with_opts_dom_pfam"/> |
29 <expand macro="thresholds_xml"/> | 29 <expand macro="thresholds_xml"/> |
30 <expand macro="cut"/> | 30 <expand macro="cut"/> |
31 <expand macro="accel_heur_xml"/> | 31 <expand macro="accel_heur_xml"/> |
32 <expand macro="adv_opts"/> | 32 <expand macro="adv_opts"/> |
33 <expand macro="seed"/> | 33 <expand macro="seed"/> |
34 </inputs> | 34 </inputs> |
35 <outputs> | 35 <outputs> |
36 <data name="output" format="txt" label="HMM matches of $hmmfile.name in $seqdb.name"/> | 36 <expand macro="output_dom_pfam" tool="PHMMER"/> |
37 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $hmmfile.name in $seqdb.name"> | |
38 <filter>oformat and 'tblout' in oformat</filter> | |
39 </data> | |
40 <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $hmmfile.name in $seqdb.name"> | |
41 <filter>oformat and 'domtblout' in oformat</filter> | |
42 </data> | |
43 <data name="pfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $hmmfile.name in $seqdb.name"> | |
44 <filter>oformat and 'pfamtblout' in oformat</filter> | |
45 </data> | |
46 </outputs> | 37 </outputs> |
47 <tests> | 38 <tests> |
48 <test> | 39 <test expect_num_outputs="4"> |
49 <param name="hmmfile" value="globins4.hmm"/> | 40 <param name="hmmfile" value="globins4.hmm"/> |
50 <param name="seqdb" value="uniprot_matches.fasta"/> | 41 <param name="seqdb" value="uniprot_matches.fasta"/> |
51 <expand macro="oformat_test" /> | 42 <expand macro="oformat_test" /> |
52 <expand macro="seed_test" /> | 43 <expand macro="seed_test" /> |
53 <output name="output" file="uniprot_globins_match.out" lines_diff="20"/> | 44 <output name="output" file="uniprot_globins_match.out" lines_diff="20"> |
54 <output name="domtblout" file="globins.domtblout" lines_diff="14"/> | 45 <expand macro="assert_out" tool="hmmsearch"/> |
55 <output name="pfamtblout" file="globins.pfamtblout" lines_diff="10"/> | 46 </output> |
56 <output name="tblout" file="globins.tblout" lines_diff="14"/> | 47 <output name="domtblout" file="globins.domtblout" lines_diff="16"> |
48 <expand macro="assert_tblout" tool="hmmsearch"/> | |
49 </output> | |
50 <output name="pfamtblout" file="globins.pfamtblout" lines_diff="12"> | |
51 <expand macro="assert_tblout" tool="hmmsearch"/> | |
52 </output> | |
53 <output name="tblout" file="globins.tblout" lines_diff="16"> | |
54 <expand macro="assert_tblout" tool="hmmsearch"/> | |
55 </output> | |
56 </test> | |
57 <test expect_num_outputs="1"> | |
58 <param name="hmmfile" value="globins4.hmm"/> | |
59 <param name="seqdb" value="uniprot_matches.fasta"/> | |
60 <expand macro="oformat_test" /> | |
61 <param name="oformat" value=""/> | |
62 <expand macro="seed_test" /> | |
63 <output name="output" file="uniprot_globins_match.out" lines_diff="20"> | |
64 <expand macro="assert_out" tool="hmmsearch"/> | |
65 </output> | |
57 </test> | 66 </test> |
58 </tests> | 67 </tests> |
59 <help><![CDATA[ | 68 <help><![CDATA[ |
60 @HELP_PRE@ | 69 @HELP_PRE@ |
61 | 70 |