Mercurial > repos > iuc > hmmer_nhmmscan
comparison nhmmscan.xml @ 4:2d406da5d34e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author | iuc |
---|---|
date | Tue, 16 Jun 2020 05:31:13 -0400 |
parents | c3075b7fdbdd |
children | 24a67ef302dd |
comparison
equal
deleted
inserted
replaced
3:f68b43be32d7 | 4:2d406da5d34e |
---|---|
8 <expand macro="stdio"/> | 8 <expand macro="stdio"/> |
9 <command><![CDATA[ | 9 <command><![CDATA[ |
10 @INPUTHMMCHOICE@ | 10 @INPUTHMMCHOICE@ |
11 nhmmscan | 11 nhmmscan |
12 | 12 |
13 @OFORMAT_WITH_OPTS_N@ | 13 @OFORMAT_WITH_OPTS@ |
14 @THRESHOLDS_NODOM@ | 14 @THRESHOLDS_NODOM@ |
15 @CUT@ | 15 @CUT@ |
16 @ACCEL_HEUR@ | 16 @ACCEL_HEUR@ |
17 --B1 $B1 | 17 --B1 $B1 |
18 --B2 $B2 | 18 --B2 $B2 |
29 ]]></command> | 29 ]]></command> |
30 <inputs> | 30 <inputs> |
31 <expand macro="input_hmm_choice" /> | 31 <expand macro="input_hmm_choice" /> |
32 <!-- todo use Galaxy features like data libraries/data tables/??? --> | 32 <!-- todo use Galaxy features like data libraries/data tables/??? --> |
33 <param name="seqfile" type="data" format="fasta" label="Sequence file"/> | 33 <param name="seqfile" type="data" format="fasta" label="Sequence file"/> |
34 <expand macro="oformat_with_opts_n"/> | 34 <expand macro="oformat_with_opts_dfam_alisc"/> |
35 <expand macro="thresholds_nodom"/> | 35 <expand macro="thresholds_nodom"/> |
36 <expand macro="cut"/> | 36 <expand macro="cut"/> |
37 <expand macro="accel_heur_xml"/> | 37 <expand macro="accel_heur_xml"/> |
38 | 38 |
39 <param argument="--B1" type="integer" value="110" label="window length for biased-composition modifier (MSV)" /> | 39 <param argument="--B1" type="integer" value="110" label="window length for biased-composition modifier (MSV)" /> |
43 <expand macro="adv_opts"/> | 43 <expand macro="adv_opts"/> |
44 <expand macro="lengths"/> | 44 <expand macro="lengths"/> |
45 <expand macro="seed"/> | 45 <expand macro="seed"/> |
46 </inputs> | 46 </inputs> |
47 <outputs> | 47 <outputs> |
48 <data name="output" format="txt" label="HMM matches of $seqfile.name against the profile database"/> | 48 <expand macro="output_dfam_alisc" tool="NHMMSCAN"/> |
49 | |
50 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database"> | |
51 <filter>oformat and 'tblout' in oformat</filter> | |
52 </data> | |
53 <data name="dfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database"> | |
54 <filter>oformat and 'dfamtblout' in oformat</filter> | |
55 </data> | |
56 <data name="aliscoresout" format="txt" label="Scores for positional matches of $seqfile.name against the profile database"> | |
57 <filter>oformat and 'aliscoresout' in oformat</filter> | |
58 </data> | |
59 </outputs> | 49 </outputs> |
60 <tests> | 50 <tests> |
61 <test> | 51 <test expect_num_outputs="3"> |
62 <param name="input_hmm_conditional|input_hmm_source" value="history"/> | 52 <param name="input_hmm_conditional|input_hmm_source" value="history"/> |
63 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/> | 53 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/> |
64 <param name="seqfile" value="dna_target.fa"/> | 54 <param name="seqfile" value="dna_target.fa"/> |
65 <expand macro="oformat_test" /> | 55 <expand macro="oformat_test" /> |
66 <expand macro="seed_test" /> | 56 <expand macro="seed_test" /> |
67 <output name="output" file="MADE1.nhmmscan_out" lines_diff="12" /> | 57 <output name="output" file="MADE1.nhmmscan_out" lines_diff="12"> |
68 <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10" /> | 58 <expand macro="assert_out" tool="nhmmscan"/> |
69 <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout" /> | 59 </output> |
70 <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" /> | 60 <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10"> |
61 <!-- nhmmscan reports as hmmscan https://github.com/EddyRivasLab/hmmer/issues/190 --> | |
62 <expand macro="assert_tblout" tool="hmmscan"/> | |
63 </output> | |
64 <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout"> | |
65 <assert_contents> | |
66 <has_line_matching expression="# hit scores"/> | |
67 </assert_contents> | |
68 </output> | |
69 <!--not test because https://github.com/EddyRivasLab/hmmer/issues/190 <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" />--> | |
71 </test> | 70 </test> |
72 </tests> | 71 </tests> |
73 <help><![CDATA[ | 72 <help><![CDATA[ |
74 @HELP_PRE@ | 73 @HELP_PRE@ |
75 | 74 |