Mercurial > repos > iuc > hmmer_jackhmmer

comparison jackhmmer.xml @ 5:5113c71c7031 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author iuc
date Tue, 16 Jun 2020 05:32:33 -0400
parents 793967b6ae8a
children d9ce554da9b4
comparison
equal deleted inserted replaced
4:793967b6ae8a 5:5113c71c7031
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