Mercurial > repos > iuc > hmmer_hmmsearch

comparison hmmsearch.xml @ 5:b774ae8e1609 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 05:27:07 -0400
parents 6867ed975e25
children 192a5046d9a2
comparison
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4:6867ed975e25 5:b774ae8e1609
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