Mercurial > repos > iuc > hmmer_jackhmmer
comparison jackhmmer.xml @ 5:5113c71c7031 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 05:32:33 -0400 |
parents | 793967b6ae8a |
children | d9ce554da9b4 |
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4:793967b6ae8a | 5:5113c71c7031 |
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7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <expand macro="stdio"/> | 8 <expand macro="stdio"/> |
9 <command><![CDATA[ | 9 <command><![CDATA[ |
10 jackhmmer | 10 jackhmmer |
11 -N $N | 11 -N $N |
12 @OFORMAT_WITH_OPTS_NOPFAM@ | 12 @OFORMAT_WITH_OPTS@ |
13 @HSSI@ | 13 @HSSI@ |
14 @THRESHOLDS@ | 14 @THRESHOLDS@ |
15 @ACCEL_HEUR@ | 15 @ACCEL_HEUR@ |
16 @ARSWS@ | 16 @ARSWS@ |
17 @AEEWS@ | 17 @AEEWS@ |
29 <inputs> | 29 <inputs> |
30 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/> | 30 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/> |
31 <!-- todo use Galaxy features like data libraries/data tables/??? --> | 31 <!-- todo use Galaxy features like data libraries/data tables/??? --> |
32 <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/> | 32 <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/> |
33 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/> | 33 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/> |
34 <expand macro="oformat_with_opts_nopfam"/> | 34 <expand macro="oformat_with_opts_dom"/> |
35 <expand macro="hssi"/> | 35 <expand macro="hssi"/> |
36 <expand macro="thresholds_xml"/> | 36 <expand macro="thresholds_xml"/> |
37 <expand macro="accel_heur_xml"/> | 37 <expand macro="accel_heur_xml"/> |
38 <expand macro="arsws"/> | 38 <expand macro="arsws"/> |
39 <expand macro="aeews"/> | 39 <expand macro="aeews"/> |
41 <expand macro="eval_calib_xml"/> | 41 <expand macro="eval_calib_xml"/> |
42 <expand macro="adv_opts"/> | 42 <expand macro="adv_opts"/> |
43 <expand macro="seed"/> | 43 <expand macro="seed"/> |
44 </inputs> | 44 </inputs> |
45 <outputs> | 45 <outputs> |
46 <data name="output" format="txt" label="JACKHMMER search of $seqfile.name in $seqdb.name"/> | 46 <expand macro="output_dom_pfam" tool="JACKHMMER"/> |
47 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name"> | |
48 <filter>oformat and 'tblout' in oformat</filter> | |
49 </data> | |
50 <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name"> | |
51 <filter>oformat and 'domtblout' in oformat</filter> | |
52 </data> | |
53 </outputs> | 47 </outputs> |
54 <tests> | 48 <tests> |
55 <test> | 49 <test expect_num_outputs="3"> |
56 <param name="seqfile" value="uniprot_matches.fasta"/> | 50 <param name="seqfile" value="uniprot_matches.fasta"/> |
57 <param name="seqdb" value="globins45.fa"/> | 51 <param name="seqdb" value="globins45.fa"/> |
58 <expand macro="oformat_test" /> | 52 <expand macro="oformat_test" /> |
59 <expand macro="seed_test" /> | 53 <expand macro="seed_test" /> |
60 <output name="output" file="jackhmmer.out" lines_diff="180"/> | 54 <output name="output" file="jackhmmer.out" lines_diff="180"> |
61 <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10"/> | 55 <expand macro="assert_out" tool="jackhmmer"/> |
62 <output name="tblout" file="jackhmmer.tblout" lines_diff="10"/> | 56 </output> |
57 <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10"> | |
58 <expand macro="assert_tblout" tool="jackhmmer"/> | |
59 </output> | |
60 <output name="tblout" file="jackhmmer.tblout" lines_diff="10"> | |
61 <expand macro="assert_tblout" tool="jackhmmer"/> | |
62 </output> | |
63 </test> | |
64 <test expect_num_outputs="1"> | |
65 <param name="seqfile" value="uniprot_matches.fasta"/> | |
66 <param name="seqdb" value="globins45.fa"/> | |
67 <expand macro="oformat_test" /> | |
68 <param name="oformat" value=""/> | |
69 <expand macro="seed_test" /> | |
70 <output name="output" file="jackhmmer.out" lines_diff="180"> | |
71 <expand macro="assert_out" tool="jackhmmer"/> | |
72 </output> | |
63 </test> | 73 </test> |
64 </tests> | 74 </tests> |
65 <help><![CDATA[ | 75 <help><![CDATA[ |
66 @HELP_PRE@ | 76 @HELP_PRE@ |
67 | 77 |