Mercurial > repos > iuc > hmmer_jackhmmer

comparison jackhmmer.xml @ 4:793967b6ae8a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
author iuc
date Mon, 11 Jun 2018 15:51:14 -0400
parents 036df14999e8
children 5113c71c7031
comparison
equal deleted inserted replaced
3:036df14999e8 4:793967b6ae8a
11 -N $N 11 -N $N
12 @OFORMAT_WITH_OPTS_NOPFAM@ 12 @OFORMAT_WITH_OPTS_NOPFAM@
13 @HSSI@ 13 @HSSI@
14 @THRESHOLDS@ 14 @THRESHOLDS@
15 @ACCEL_HEUR@ 15 @ACCEL_HEUR@
16 @MCSS@
17 @ARSWS@ 16 @ARSWS@
18 @AEEWS@ 17 @AEEWS@
19 @PRIOR@ 18 @PRIOR@
20 19
21 @EVAL_CALIB@ 20 @EVAL_CALIB@
34 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/> 33 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
35 <expand macro="oformat_with_opts_nopfam"/> 34 <expand macro="oformat_with_opts_nopfam"/>
36 <expand macro="hssi"/> 35 <expand macro="hssi"/>
37 <expand macro="thresholds_xml"/> 36 <expand macro="thresholds_xml"/>
38 <expand macro="accel_heur_xml"/> 37 <expand macro="accel_heur_xml"/>
39 <expand macro="mcss"/>
40 <expand macro="arsws"/> 38 <expand macro="arsws"/>
41 <expand macro="aeews"/> 39 <expand macro="aeews"/>
42 <expand macro="prior"/> 40 <expand macro="prior"/>
43 <expand macro="eval_calib_xml"/> 41 <expand macro="eval_calib_xml"/>
44 <expand macro="adv_opts"/> 42 <expand macro="adv_opts"/>
45 <expand macro="seed"/> 43 <expand macro="seed"/>
46 </inputs> 44 </inputs>
47 <outputs> 45 <outputs>
48 <data name="output" format="txt" label="PHMMER search of $seqfile.name in $seqdb.name"/> 46 <data name="output" format="txt" label="JACKHMMER search of $seqfile.name in $seqdb.name"/>
49 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name"> 47 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
50 <filter>oformat and 'tblout' in oformat</filter> 48 <filter>oformat and 'tblout' in oformat</filter>
51 </data> 49 </data>
52 <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name"> 50 <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
53 <filter>oformat and 'domtblout' in oformat</filter> 51 <filter>oformat and 'domtblout' in oformat</filter>
80 78
81 @OFORMAT_WITH_OPTS_HELP_NOPFAM@ 79 @OFORMAT_WITH_OPTS_HELP_NOPFAM@
82 @HSSI_HELP@ 80 @HSSI_HELP@
83 @THRESHOLDS_HELP@ 81 @THRESHOLDS_HELP@
84 @ACCEL_HEUR_HELP@ 82 @ACCEL_HEUR_HELP@
85 @MCSS_HELP@
86 @ARSWS_HELP@ 83 @ARSWS_HELP@
87 @AEEWS_HELP@ 84 @AEEWS_HELP@
88 @PRIOR_HELP@ 85 @PRIOR_HELP@
89 @EVAL_CALIB_HELP@ 86 @EVAL_CALIB_HELP@
90 @ADV_OPTS_HELP@ 87 @ADV_OPTS_HELP@