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comparison hmmbuild.xml @ 0:fb8582aff5db draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
author iuc
date Sat, 25 Jun 2016 15:04:58 -0400
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children 7ea31fc35394
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-1:000000000000 0:fb8582aff5db
1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmbuild" name="hmmbuild" version="@WRAPPER_VERSION@.0">
3 <description>Build a profile HMM from an input multiple alignment</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 hmmbuild
11
12 #if $hmmname:
13 -n "$hmmname"
14 #end if
15
16 @FORMAT_SELECTOR@
17 @MCSS@
18 @ARSWS@
19 @AEEWS@
20 @PRIOR@
21 @HSSI@
22 @EVAL_CALIB@
23
24 @CPU@
25 @SEED@
26
27 @LENGTHS@
28 #if $maxinsertlen:
29 --maxinsertlen $maxinsertlen
30 #end if
31
32 $hmmout
33 $msafile
34 ]]></command>
35 <inputs>
36 <expand macro="input_msa" />
37 <param name="hmmname" type="text" optional="True" label="Name for the HMM" help="(-n)"/>
38 <expand macro="format_selector"/>
39 <expand macro="mcss"/>
40 <expand macro="arsws"/>
41 <expand macro="aeews"/>
42 <expand macro="prior"/>
43 <expand macro="hssi"/>
44 <expand macro="eval_calib_xml"/>
45 <expand macro="seed"/>
46
47 <expand macro="lengths" />
48 <param name="maxinsertlen" label="Pretend all inserts are length &lt;= n"
49 help="(--maxinsertlen)" optional="True" type="integer"/>
50 </inputs>
51 <outputs>
52 <data format="hmm3" name="hmmout" label="HMM profile from $msafile.name"/>
53 </outputs>
54 <tests>
55 <test>
56 <param name="msafile" value="globins4.sto"/>
57 <expand macro="seed_test" />
58 <output name="hmmout" file="globins4.hmm" lines_diff="10"/>
59 </test>
60 <test>
61 <param name="msafile" value="MADE1.sto"/>
62 <param name="input_format_select" value="--dna"/>
63 <expand macro="seed_test" />
64 <output name="hmmout" file="MADE1.hmm" lines_diff="14"/>
65 </test>
66 </tests>
67 <help><![CDATA[
68 @HELP_PRE@
69
70 For each multiple sequence alignment in <msafile> build a profile HMM and save
71 it to a new file <hmmfile out>.
72
73 @HELP_PRE_OTH@
74
75 @FORMAT_SELECTOR_HELP@
76 @MCSS_HELP@
77 @ARSWS_HELP@
78 @AEEWS_HELP@
79 @PRIOR_HELP@
80 @HSSI_HELP@
81 @EVAL_CALIB_HELP@
82 @SEED_HELP@
83 @LENGTHS_HELP@
84
85 @ATTRIBUTION@
86 ]]></help>
87 <expand macro="citation"/>
88 </tool>