Mercurial > repos > iuc > hmmer_alimask

annotate alimask.xml @ 8:3734a6ad6363 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 061757dd7b3bfe66b7738fd54bd6c5e135d9afe8
author iuc
date Mon, 06 Nov 2023 20:25:57 +0000
parents b4dc65565864
children e3e5f208e93c
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a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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1 <?xml version="1.0"?>
3
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2 <tool id="hmmer_alimask" name="alimask" version="@TOOL_VERSION@">
8
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3 <description>append modelmask line to a multiple sequence alignments</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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11 alimask
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12
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13 #if $range_type.range_type_select == "model":
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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14 #set range = ','.join( [ "%s-%s" % (str($range.modelrangestart), str($range.modelrangeend)) for $range in $range_type.modelranges])
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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15 --modelrange $range
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16 #else
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17 #set range = ','.join( [ "%s-%s" % (str($range.alirangestart), str($range.alirangeend)) for $range in $range_type.aliranges])
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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18 --alirange $range
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19 #end if
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20
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21 @FORMAT_SELECTOR@
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22 @MCSS@
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23 @ARSWS@
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24 @SEED@
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25
3
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26 '$msafile'
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27 '$output'
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28 ]]></command>
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29 <inputs>
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30 <expand macro="input_msa" />
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31 <conditional name="range_type">
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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32 <param name="range_type_select" type="select"
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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33 label="Input range coordinate basis">
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34 <option value="model">Range in model coordinates</option>
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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35 <option value="ali">Range in alignment coordinates</option>
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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36 </param>
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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37 <when value="model">
3
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38 <repeat name="modelranges" min="1" title="Model Ranges">
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39 <param name="modelrangestart" type="integer" value="10" label="Model Range Start" />
819d044451ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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40 <param name="modelrangeend" type="integer" value="20" label="Model Range End" />
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41 </repeat>
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42 </when>
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43 <when value="ali">
3
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44 <repeat name="aliranges" min="1" title="Alignment Ranges">
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45 <param name="alirangestart" type="integer" value="10" label="Alignment Range Start" />
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46 <param name="alirangeend" type="integer" value="20" label="Alignment Range End" />
0
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47 </repeat>
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48 </when>
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49 </conditional>
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50
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51 <!-- TODO: support model2ali/ali2model as separate utilities? -->
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52 <expand macro="format_selector"/>
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53 <expand macro="mcss"/>
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54 <expand macro="arsws"/>
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55 <expand macro="seed"/>
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56 </inputs>
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57 <outputs>
3
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58 <data name="output" format="stockholm" label="Output MSA"/>
0
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="msafile" value="globins4.sto"/>
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63 <param name="modelrangestart" value="10" />
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64 <param name="modelrangeend" value="20" />
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65 <expand macro="seed_test" />
5
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66 <output name="output" file="globins-masked.sto" lines_diff="4">
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67 <assert_contents>
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68 <has_line_matching expression="# STOCKHOLM.*"/>
b4dc65565864 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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69 <has_line_matching expression="//"/>
b4dc65565864 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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70 </assert_contents>
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71 </output>
0
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 @HELP_PRE@
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76
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77 alimask is used to apply a mask line to a multiple sequence alignment, based on
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78 provided alignment or model coordinates. When hmmbuild receives a masked
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79 alignment as input, it produces a profile model in which the emission
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80 probabilities at masked positions are set to match the background frequency,
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81 rather than being set based on observed frequencies in the alignment.
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82 Position-specific insertion and deletion rates are not altered, even in masked
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83 regions. alimask autodetects input format, and produces masked alignments in
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84 Stockholm format. <msafile> may contain only one sequence alignment.
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85
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86 A common motivation for masking a region in an alignment is that the region
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87 contains a simple tandem repeat that is observed to cause an unacceptably high
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88 rate of false positive hits.
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89
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90 In the simplest case, a mask range is given in coordinates relative to the
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91 input alignment, using --alirange <s>. However it is more often the case that
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92 the region to be masked has been identified in coordinates relative to the
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93 profile model (e.g. based on recognizing a simple repeat pattern in false hit
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94 alignments or in the HMM logo). Not all alignment columns are converted to
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95 match state positions in the profile (see the --symfrac flag for hmmbuild for
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96 discussion), so model positions do not necessarily match up to alignment column
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97 positions. To remove the burden of converting model positions to alignment
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98 positions, alimask accepts the mask range input in model coordinates as well,
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99 using --modelrange <s>. When using this flag, alimask determines which
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100 alignment positions would be identified by hmmbuild as match states, a process
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101 that requires that all hmmbuild flags impacting that decision be supplied to
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102 alimask. It is for this reason that many of the hmmbuild flags are also used by
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103 alimask.
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104
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105 @HELP_PRE_OTH@
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106
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107 **Ranges**
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108
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109 Ranges are expressed as a hyphenated pair of integers, e.g. 12-40. Ranges can
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110 be expressed in terms of model coordinates or alignment coordinates.
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111
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112 @FORMAT_SELECTOR_HELP@
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113 @MCSS_HELP@
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114 @ARSWS_HELP@
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115 @SEED_HELP@
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116
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117 @ATTRIBUTION@
3
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118 ]]></help>
0
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119 <expand macro="citation"/>
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120 </tool>