Mercurial > repos > iuc > hmmer_nhmmscan

comparison nhmmscan.xml @ 4:2d406da5d34e 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 05:31:13 -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