Mercurial > repos > iuc > hmmer_hmmscan

comparison hmmscan.xml @ 3:1a83249ddfff 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 03:51:55 -0400
parents b49a4465041d
children be7097d6e3ff
comparison
equal deleted inserted replaced
2:25fa92aa34c0 3:1a83249ddfff
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.1"> 2 <tool id="hmmer_hmmscan" name="hmmscan" version="@TOOL_VERSION@">
3 <description>search sequence(s) against a profile database</description> 3 <description>search protein sequence(s) against a protein 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 #if $input_hmm_conditional.input_hmm_source == "history": 10 @INPUTHMMCHOICE@
11 ## "Press" database
12 hmmpress '$input_hmm_conditional.hmmfile' &&
13 #end if
14 ## Scan
15 hmmscan 11 hmmscan
16 12
17 @OFORMAT_WITH_OPTS@ 13 @OFORMAT_WITH_OPTS@
18 @THRESHOLDS@ 14 @THRESHOLDS@
19 @CUT@ 15 @CUT@
20 @ACCEL_HEUR@ 16 @ACCEL_HEUR@
21 @ADV_OPTS@ 17 @ADV_OPTS@
22 @CPU@ 18 @CPU@
23 @SEED@ 19 @SEED@
24 20
25 @INPUTHMMCHOICE@ 21 '$input_hmm_filename'
26 '$seqfile' 22 '$seqfile'
27 > '$output' 23 > '$output'
28 #if $input_hmm_conditional.input_hmm_source == "history": 24 ]]></command>
29 ## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype
30 && rm '${input_hmm_conditional.hmmfile}.h3m' '${input_hmm_conditional.hmmfile}.h3i' '${input_hmm_conditional.hmmfile}.h3f' '${input_hmm_conditional.hmmfile}.h3p';
31 #end if
32 ]]></command>
33 <inputs> 25 <inputs>
34 <expand macro="input_hmm_choice" /> 26 <expand macro="input_hmm_choice" />
35 <!-- todo use Galaxy features like data libraries/data tables/??? --> 27 <!-- todo use Galaxy features like data libraries/data tables/??? -->
36 <param name="seqfile" type="data" format="fasta" label="Sequence file"/> 28 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
37 <expand macro="oformat_with_opts"/> 29 <expand macro="oformat_with_opts"/>
40 <expand macro="accel_heur_xml"/> 32 <expand macro="accel_heur_xml"/>
41 <expand macro="adv_opts"/> 33 <expand macro="adv_opts"/>
42 <expand macro="seed"/> 34 <expand macro="seed"/>
43 </inputs> 35 </inputs>
44 <outputs> 36 <outputs>
45 <data format="txt" name="output" label="HMM matches of $seqfile.name against the profile database"/> 37 <data name="output" format="txt" label="HMM matches of $seqfile.name against the profile database"/>
46 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database"> 38 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database">
47 <filter>'tblout' in oformat</filter> 39 <filter>oformat and 'tblout' in oformat</filter>
48 </data> 40 </data>
49 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name against the profile database"> 41 <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name against the profile database">
50 <filter>'domtblout' in oformat</filter> 42 <filter>oformat and 'domtblout' in oformat</filter>
51 </data> 43 </data>
52 <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database"> 44 <data name="pfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
53 <filter>'pfamtblout' in oformat</filter> 45 <filter>oformat and 'pfamtblout' in oformat</filter>
54 </data> 46 </data>
55 </outputs> 47 </outputs>
56 <tests> 48 <tests>
57 <test> 49 <test>
58 <param name="input_hmm_conditional|input_hmm_source" value="history"/> 50 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
59 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/> 51 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
60 <param name="seqfile" value="dna_target.fa"/> 52 <param name="seqfile" value="dna_target.fa"/>
61 <expand macro="oformat_test" /> 53 <expand macro="oformat_test" />
62 <expand macro="seed_test" /> 54 <expand macro="seed_test" />
63 <output name="output" file="MADE1.out" lines_diff="24"/> 55 <output name="output" file="MADE1.out" lines_diff="24"/>
64 <output name="tblout" file="MADE1.out.tblout" lines_diff="20"/> 56 <output name="tblout" file="MADE1.out.tblout" lines_diff="14"/>
65 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="20"/> 57 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="10"/>
66 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="20"/> 58 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="10"/>
67 </test> 59 </test>
68 </tests> 60 </tests>
69 <help><![CDATA[ 61 <help><![CDATA[
70 @HELP_PRE@ 62 @HELP_PRE@
71 63
82 @ACCEL_HEUR_HELP@ 74 @ACCEL_HEUR_HELP@
83 @ADV_OPTS_HELP@ 75 @ADV_OPTS_HELP@
84 @SEED_HELP@ 76 @SEED_HELP@
85 77
86 @ATTRIBUTION@ 78 @ATTRIBUTION@
87 ]]></help> 79 ]]></help>
88 <expand macro="citation"/> 80 <expand macro="citation"/>
89 </tool> 81 </tool>