Mercurial > repos > iuc > hmmer_hmmscan

comparison hmmscan.xml @ 7:d02bc72e520b 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 09:23:51 +0000
parents 8e797aaf03fb
children 63f1dd395c05
comparison
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6:d52b0e4bfa46 7:d02bc72e520b
24 ]]></command> 24 ]]></command>
25 <inputs> 25 <inputs>
26 <expand macro="input_hmm_choice" /> 26 <expand macro="input_hmm_choice" />
27 <!-- todo use Galaxy features like data libraries/data tables/??? --> 27 <!-- todo use Galaxy features like data libraries/data tables/??? -->
28 <param name="seqfile" type="data" format="fasta" label="Sequence file"/> 28 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
29 <expand macro="oformat_with_opts"/> 29 <expand macro="oformat_with_opts_dom_pfam"/>
30 <expand macro="thresholds_xml"/> 30 <expand macro="thresholds_xml"/>
31 <expand macro="cut"/> 31 <expand macro="cut"/>
32 <expand macro="accel_heur_xml"/> 32 <expand macro="accel_heur_xml"/>
33 <expand macro="adv_opts"/> 33 <expand macro="adv_opts"/>
34 <expand macro="seed"/> 34 <expand macro="seed"/>
35 </inputs> 35 </inputs>
36 <outputs> 36 <outputs>
37 <data name="output" format="txt" label="HMM matches of $seqfile.name against the profile database"/> 37 <expand macro="output_dom_pfam" tool="HMMSCAN"/>
38 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database">
39 <filter>oformat and 'tblout' in oformat</filter>
40 </data>
41 <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name against the profile database">
42 <filter>oformat and 'domtblout' in oformat</filter>
43 </data>
44 <data name="pfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
45 <filter>oformat and 'pfamtblout' in oformat</filter>
46 </data>
47 </outputs> 38 </outputs>
48 <tests> 39 <tests>
49 <test> 40 <test expect_num_outputs="4">
50 <param name="input_hmm_conditional|input_hmm_source" value="history"/> 41 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
51 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/> 42 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
52 <param name="seqfile" value="dna_target.fa"/> 43 <param name="seqfile" value="dna_target.fa"/>
53 <expand macro="oformat_test" /> 44 <expand macro="oformat_test" />
54 <expand macro="seed_test" /> 45 <expand macro="seed_test" />
55 <output name="output" file="MADE1.out" lines_diff="24"/> 46 <output name="output" file="MADE1.out" lines_diff="24">
56 <output name="tblout" file="MADE1.out.tblout" lines_diff="14"/> 47 <expand macro="assert_out" tool="hmmscan"/>
57 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="10"/> 48 </output>
58 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="10"/> 49 <output name="tblout" file="MADE1.out.tblout" lines_diff="14">
50 <expand macro="assert_tblout" tool="hmmscan"/>
51 </output>
52 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="10">
53 <expand macro="assert_tblout" tool="hmmscan"/>
54 </output>
55 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="10">
56 <expand macro="assert_tblout" tool="hmmscan"/>
57 </output>
59 </test> 58 </test>
60 </tests> 59 </tests>
61 <help><![CDATA[ 60 <help><![CDATA[
62 @HELP_PRE@ 61 @HELP_PRE@
63 62