Mercurial > repos > iuc > hmmer_hmmbuild
comparison hmmbuild.xml @ 3:7ea31fc35394 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author | iuc |
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date | Sat, 07 Apr 2018 03:51:18 -0400 |
parents | fb8582aff5db |
children | 750269125dc9 |
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2:691cd6c40568 | 3:7ea31fc35394 |
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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 <= n" | 48 <param argument="--maxinsertlen" type="integer" optional="true" label="Pretend all inserts are length <= 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> |