Mercurial > repos > iuc > hmmer_nhmmscan

comparison nhmmscan.xml @ 2:c3075b7fdbdd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:49:11 -0400
parents a6098dd0cb46
children 2d406da5d34e
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1:4351ee79c942 2:c3075b7fdbdd
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_nhmmscan" name="nhmmscan" version="@WRAPPER_VERSION@.0"> 2 <tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@">
3 <description>search DNA sequence(s) against a DNA profile database</description> 3 <description>search DNA sequence(s) against a DNA profile database</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 hmmpress $hmmfile; 10 @INPUTHMMCHOICE@
11
12 nhmmscan 11 nhmmscan
13 12
14 @OFORMAT_WITH_OPTS_N@ 13 @OFORMAT_WITH_OPTS_N@
15 @THRESHOLDS_NODOM@ 14 @THRESHOLDS_NODOM@
16 @CUT@ 15 @CUT@
22 @ADV_OPTS@ 21 @ADV_OPTS@
23 @LENGTHS@ 22 @LENGTHS@
24 @CPU@ 23 @CPU@
25 @SEED@ 24 @SEED@
26 25
27 $hmmfile 26 '$input_hmm_filename'
28 $seqfile 27 '$seqfile'
29 > $output 28 > '$output'
30 ]]></command> 29 ]]></command>
31 <inputs> 30 <inputs>
32 <expand macro="input_hmm" /> 31 <expand macro="input_hmm_choice" />
33 <!-- todo use Galaxy features like data libraries/data tables/??? --> 32 <!-- todo use Galaxy features like data libraries/data tables/??? -->
34 <param name="seqfile" type="data" format="fasta" label="Sequence file"/> 33 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
35 <expand macro="oformat_with_opts_n"/> 34 <expand macro="oformat_with_opts_n"/>
36 <expand macro="thresholds_nodom"/> 35 <expand macro="thresholds_nodom"/>
37 <expand macro="cut"/> 36 <expand macro="cut"/>
38 <expand macro="accel_heur_xml"/> 37 <expand macro="accel_heur_xml"/>
39 38
40 <param name="B1" type="integer" label="window length for biased-composition modifier (MSV)" help="(--B1)" value="110"/> 39 <param argument="--B1" type="integer" value="110" label="window length for biased-composition modifier (MSV)" />
41 <param name="B2" type="integer" label="window length for biased-composition modifier (Vit)" help="(--B2)" value="240"/> 40 <param argument="--B2" type="integer" value="240" label="window length for biased-composition modifier (Vit)" />
42 <param name="B3" type="integer" label="window length for biased-composition modifier (Fwd)" help="(--B3)" value="1000"/> 41 <param argument="--B3" type="integer" value="1000" label="window length for biased-composition modifier (Fwd)" />
43 42
44 <expand macro="adv_opts"/> 43 <expand macro="adv_opts"/>
45 <expand macro="lengths"/> 44 <expand macro="lengths"/>
46 <expand macro="seed"/> 45 <expand macro="seed"/>
47 </inputs> 46 </inputs>
48 <outputs> 47 <outputs>
49 <data format="txt" name="output" label="HMM matches of $seqfile.name in $hmmfile.name"/> 48 <data name="output" format="txt" label="HMM matches of $seqfile.name against the profile database"/>
50 49
51 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name"> 50 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database">
52 <filter>'tblout' in str(oformat)</filter> 51 <filter>oformat and 'tblout' in oformat</filter>
53 </data> 52 </data>
54 <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name"> 53 <data name="dfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
55 <filter>'pfamtblout' in str(oformat)</filter> 54 <filter>oformat and 'dfamtblout' in oformat</filter>
56 </data> 55 </data>
57 <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name"> 56 <data name="aliscoresout" format="txt" label="Scores for positional matches of $seqfile.name against the profile database">
58 <filter>'aliscoresout' in str(oformat)</filter> 57 <filter>oformat and 'aliscoresout' in oformat</filter>
59 </data> 58 </data>
60 </outputs> 59 </outputs>
61 <tests> 60 <tests>
62 <test> 61 <test>
63 <param name="hmmfile" value="MADE1.hmm"/> 62 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
63 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
64 <param name="seqfile" value="dna_target.fa"/> 64 <param name="seqfile" value="dna_target.fa"/>
65 <expand macro="oformat_test" /> 65 <expand macro="oformat_test" />
66 <expand macro="seed_test" /> 66 <expand macro="seed_test" />
67 <output name="output" file="MADE1.out" lines_diff="140"/> 67 <output name="output" file="MADE1.nhmmscan_out" lines_diff="12" />
68 <output name="tblout" file="MADE1.out.tblout" lines_diff="30"/> 68 <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10" />
69 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="30"/> 69 <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout" />
70 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="36"/> 70 <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" />
71 </test> 71 </test>
72 </tests> 72 </tests>
73 <help><![CDATA[ 73 <help><![CDATA[
74 @HELP_PRE@ 74 @HELP_PRE@
75 75