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comparison alimask.xml @ 0:62479bdcc059 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
author iuc
date Tue, 12 May 2015 15:04:26 -0400
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-1:000000000000 0:62479bdcc059
1 <?xml version="1.0"?>
2 <tool id="hmmer_alimask" name="alimask" version="@WRAPPER_VERSION@.0">
3 <description>append modelmask line to a multiple sequence alignments</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10
11 alimask
12
13 #if $range_type.range_type_select == "model":
14 #set range = ','.join( [ "%s-%s" % (str($range.modelrangestart), str($range.modelrangeend)) for $range in $range_type.modelranges])
15 --modelrange $range
16 #else
17 #set range = ','.join( [ "%s-%s" % (str($range.alirangestart), str($range.alirangeend)) for $range in $range_type.aliranges])
18 --alirange $range
19 #end if
20
21 @FORMAT_SELECTOR@
22 @MCSS@
23 @ARSWS@
24 @SEED@
25
26 $msafile
27 $output
28 ]]></command>
29 <inputs>
30 <expand macro="input_msa" />
31 <conditional name="range_type">
32 <param name="range_type_select" type="select"
33 label="Input range coordinate basis">
34 <option value="model">Range in model coordinates</option>
35 <option value="ali">Range in alignment coordinates</option>
36 </param>
37 <when value="model">
38 <repeat min="1" name="modelranges" title="Model Ranges">
39 <param label="Model Range Start" name="modelrangestart" type="integer" value="10" />
40 <param label="Model Range End" name="modelrangeend" type="integer" value="20" />
41 </repeat>
42 </when>
43 <when value="ali">
44 <repeat min="1" name="aliranges" title="Alignment Ranges">
45 <param label="Alignment Range Start" name="alirangestart" type="integer" value="10" />
46 <param label="Alignment Range End" name="alirangeend" type="integer" value="20" />
47 </repeat>
48 </when>
49 </conditional>
50
51 <!-- TODO: support model2ali/ali2model as separate utilities? -->
52 <expand macro="format_selector"/>
53 <expand macro="mcss"/>
54 <expand macro="arsws"/>
55 <expand macro="seed"/>
56 </inputs>
57 <outputs>
58 <data format="stockholm" name="output" label="Output MSA"/>
59 </outputs>
60 <tests>
61 <test>
62 <param name="msafile" value="globins4.sto"/>
63 <param name="modelrangestart" value="10" />
64 <param name="modelrangeend" value="20" />
65 <expand macro="seed_test" />
66 <output name="output" file="globins-masked.sto" lines_diff="4"/>
67 </test>
68 </tests>
69 <help><![CDATA[
70 @HELP_PRE@
71
72 alimask is used to apply a mask line to a multiple sequence alignment, based on
73 provided alignment or model coordinates. When hmmbuild receives a masked
74 alignment as input, it produces a profile model in which the emission
75 probabilities at masked positions are set to match the background frequency,
76 rather than being set based on observed frequencies in the alignment.
77 Position-specific insertion and deletion rates are not altered, even in masked
78 regions. alimask autodetects input format, and produces masked alignments in
79 Stockholm format. <msafile> may contain only one sequence alignment.
80
81 A common motivation for masking a region in an alignment is that the region
82 contains a simple tandem repeat that is observed to cause an unacceptably high
83 rate of false positive hits.
84
85 In the simplest case, a mask range is given in coordinates relative to the
86 input alignment, using --alirange <s>. However it is more often the case that
87 the region to be masked has been identified in coordinates relative to the
88 profile model (e.g. based on recognizing a simple repeat pattern in false hit
89 alignments or in the HMM logo). Not all alignment columns are converted to
90 match state positions in the profile (see the --symfrac flag for hmmbuild for
91 discussion), so model positions do not necessarily match up to alignment column
92 positions. To remove the burden of converting model positions to alignment
93 positions, alimask accepts the mask range input in model coordinates as well,
94 using --modelrange <s>. When using this flag, alimask determines which
95 alignment positions would be identified by hmmbuild as match states, a process
96 that requires that all hmmbuild flags impacting that decision be supplied to
97 alimask. It is for this reason that many of the hmmbuild flags are also used by
98 alimask.
99
100 @HELP_PRE_OTH@
101
102 **Ranges**
103
104 Ranges are expressed as a hyphenated pair of integers, e.g. 12-40. Ranges can
105 be expressed in terms of model coordinates or alignment coordinates.
106
107 @FORMAT_SELECTOR_HELP@
108 @MCSS_HELP@
109 @ARSWS_HELP@
110 @SEED_HELP@
111
112 @ATTRIBUTION@
113 ]]></help>
114 <expand macro="citation"/>
115 </tool>