Mercurial > repos > iuc > hmmer_hmmbuild

comparison hmmbuild.xml @ 3:7ea31fc35394 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 03:51:18 -0400
parents fb8582aff5db
children 750269125dc9
comparison
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2:691cd6c40568 3:7ea31fc35394
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmbuild" name="hmmbuild" version="@WRAPPER_VERSION@.0"> 2 <tool id="hmmer_hmmbuild" name="hmmbuild" version="@TOOL_VERSION@">
3 <description>Build a profile HMM from an input multiple alignment</description> 3 <description>Build a profile HMM from an input multiple alignment</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 hmmbuild 10 hmmbuild
11 11
12 #if $hmmname: 12 #if $hmmname:
13 -n "$hmmname" 13 -n '$hmmname'
14 #end if 14 #end if
15 15
16 @FORMAT_SELECTOR@ 16 @FORMAT_SELECTOR@
17 @MCSS@ 17 @MCSS@
18 @ARSWS@ 18 @ARSWS@
23 23
24 @CPU@ 24 @CPU@
25 @SEED@ 25 @SEED@
26 26
27 @LENGTHS@ 27 @LENGTHS@
28 #if $maxinsertlen: 28 #if str($maxinsertlen):
29 --maxinsertlen $maxinsertlen 29 --maxinsertlen $maxinsertlen
30 #end if 30 #end if
31 31
32 $hmmout 32 '$hmmout'
33 $msafile 33 '$msafile'
34 ]]></command> 34 ]]></command>
35 <inputs> 35 <inputs>
36 <expand macro="input_msa" /> 36 <expand macro="input_msa" />
37 <param name="hmmname" type="text" optional="True" label="Name for the HMM" help="(-n)"/> 37 <param name="hmmname" argument="-n" type="text" optional="true" label="Name for the HMM" />
38 <expand macro="format_selector"/> 38 <expand macro="format_selector"/>
39 <expand macro="mcss"/> 39 <expand macro="mcss"/>
40 <expand macro="arsws"/> 40 <expand macro="arsws"/>
41 <expand macro="aeews"/> 41 <expand macro="aeews"/>
42 <expand macro="prior"/> 42 <expand macro="prior"/>
43 <expand macro="hssi"/> 43 <expand macro="hssi"/>
44 <expand macro="eval_calib_xml"/> 44 <expand macro="eval_calib_xml"/>
45 <expand macro="seed"/> 45 <expand macro="seed"/>
46 46
47 <expand macro="lengths" /> 47 <expand macro="lengths" />
48 <param name="maxinsertlen" label="Pretend all inserts are length &lt;= n" 48 <param argument="--maxinsertlen" type="integer" optional="true" label="Pretend all inserts are length &lt;= n" />
49 help="(--maxinsertlen)" optional="True" type="integer"/>
50 </inputs> 49 </inputs>
51 <outputs> 50 <outputs>
52 <data format="hmm3" name="hmmout" label="HMM profile from $msafile.name"/> 51 <data name="hmmout" format="hmm3" label="HMM profile from $msafile.name"/>
53 </outputs> 52 </outputs>
54 <tests> 53 <tests>
55 <test> 54 <test>
56 <param name="msafile" value="globins4.sto"/> 55 <param name="msafile" value="globins4.sto"/>
57 <expand macro="seed_test" /> 56 <expand macro="seed_test" />
81 @EVAL_CALIB_HELP@ 80 @EVAL_CALIB_HELP@
82 @SEED_HELP@ 81 @SEED_HELP@
83 @LENGTHS_HELP@ 82 @LENGTHS_HELP@
84 83
85 @ATTRIBUTION@ 84 @ATTRIBUTION@
86 ]]></help> 85 ]]></help>
87 <expand macro="citation"/> 86 <expand macro="citation"/>
88 </tool> 87 </tool>