Mercurial > repos > iuc > hmmer_hmmscan

comparison hmmscan.xml @ 3:4a09810b41ea draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
author iuc
date Mon, 14 Nov 2016 15:08:35 -0500
parents 6313ad2f168f
children 8e797aaf03fb
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2:6313ad2f168f 3:4a09810b41ea
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.0"> 2 <tool id="hmmer_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.1">
3 <description>search sequence(s) against a profile database</description> 3 <description>search sequence(s) against a 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 ## "Press" database 10 #if $input_hmm_conditional.input_hmm_source == "history":
11 hmmpress $hmmfile; 11 ## "Press" database
12 hmmpress '$input_hmm_conditional.hmmfile' &&
13 #end if
12 ## Scan 14 ## Scan
13 hmmscan 15 hmmscan
14 16
15 @OFORMAT_WITH_OPTS@ 17 @OFORMAT_WITH_OPTS@
16 @THRESHOLDS@ 18 @THRESHOLDS@
18 @ACCEL_HEUR@ 20 @ACCEL_HEUR@
19 @ADV_OPTS@ 21 @ADV_OPTS@
20 @CPU@ 22 @CPU@
21 @SEED@ 23 @SEED@
22 24
23 $hmmfile 25 @INPUTHMMCHOICE@
24 $seqfile 26 '$seqfile'
25 > $output; 27 > '$output'
26 ## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype 28 #if $input_hmm_conditional.input_hmm_source == "history":
27 rm ${hmmfile}.h3m ${hmmfile}.h3i ${hmmfile}.h3f ${hmmfile}.h3p; 29 ## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype
30 && rm '${input_hmm_conditional.hmmfile}.h3m' '${input_hmm_conditional.hmmfile}.h3i' '${input_hmm_conditional.hmmfile}.h3f' '${input_hmm_conditional.hmmfile}.h3p';
31 #end if
28 ]]></command> 32 ]]></command>
29 <inputs> 33 <inputs>
30 <expand macro="input_hmm" /> 34 <expand macro="input_hmm_choice" />
31 <!-- todo use Galaxy features like data libraries/data tables/??? --> 35 <!-- todo use Galaxy features like data libraries/data tables/??? -->
32 <param name="seqfile" type="data" format="fasta" label="Sequence file"/> 36 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
33 <expand macro="oformat_with_opts"/> 37 <expand macro="oformat_with_opts"/>
34 <expand macro="thresholds_xml"/> 38 <expand macro="thresholds_xml"/>
35 <expand macro="cut"/> 39 <expand macro="cut"/>
36 <expand macro="accel_heur_xml"/> 40 <expand macro="accel_heur_xml"/>
37 <expand macro="adv_opts"/> 41 <expand macro="adv_opts"/>
38 <expand macro="seed"/> 42 <expand macro="seed"/>
39 </inputs> 43 </inputs>
40 <outputs> 44 <outputs>
41 <data format="txt" name="output" label="HMM matches of $seqfile.name in $hmmfile.name"/> 45 <data format="txt" name="output" label="HMM matches of $seqfile.name against the profile database"/>
42 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name"> 46 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database">
43 <filter>'tblout' in oformat</filter> 47 <filter>'tblout' in oformat</filter>
44 </data> 48 </data>
45 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $hmmfile.name"> 49 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name against the profile database">
46 <filter>'domtblout' in oformat</filter> 50 <filter>'domtblout' in oformat</filter>
47 </data> 51 </data>
48 <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name"> 52 <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
49 <filter>'pfamtblout' in oformat</filter> 53 <filter>'pfamtblout' in oformat</filter>
50 </data> 54 </data>
51 </outputs> 55 </outputs>
52 <tests> 56 <tests>
53 <test> 57 <test>
54 <param name="hmmfile" value="MADE1.hmm"/> 58 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
59 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
55 <param name="seqfile" value="dna_target.fa"/> 60 <param name="seqfile" value="dna_target.fa"/>
56 <expand macro="oformat_test" /> 61 <expand macro="oformat_test" />
57 <expand macro="seed_test" /> 62 <expand macro="seed_test" />
58 <output name="output" file="MADE1.out" lines_diff="24"/> 63 <output name="output" file="MADE1.out" lines_diff="24"/>
59 <output name="tblout" file="MADE1.out.tblout" lines_diff="20"/> 64 <output name="tblout" file="MADE1.out.tblout" lines_diff="20"/>