Mercurial > repos > iuc > hmmer_alimask

annotate alimask.xml @ 9:e3e5f208e93c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 721504306833ba97c91f285e5bfd86efc04875ee
author iuc
date Sun, 25 Feb 2024 18:32:14 +0000
parents 3734a6ad6363
children
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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"?>
9
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2 <tool id="hmmer_alimask" name="alimask" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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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 <command detect_errors="aggressive"><![CDATA[
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10 alimask
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12 #if $range_type.range_type_select == "model":
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13 #set range = ','.join( [ "%s-%s" % (str($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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14 --modelrange $range
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15 #else
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16 #set range = ','.join( [ "%s-%s" % (str($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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17 --alirange $range
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18 #end if
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20 @FORMAT_SELECTOR@
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21 @MCSS@
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22 @ARSWS@
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23 @SEED@
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24
3
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25 '$msafile'
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26 '$output'
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27 ]]></command>
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28 <inputs>
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29 <expand macro="input_msa" />
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30 <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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31 <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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32 label="Input range coordinate basis">
a20b2c7c5eee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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33 <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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34 <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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35 </param>
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36 <when value="model">
3
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37 <repeat name="modelranges" min="1" title="Model Ranges">
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38 <param name="modelrangestart" type="integer" value="10" label="Model Range Start" />
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39 <param name="modelrangeend" type="integer" value="20" label="Model Range End" />
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40 </repeat>
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41 </when>
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42 <when value="ali">
3
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43 <repeat name="aliranges" min="1" title="Alignment Ranges">
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44 <param name="alirangestart" type="integer" value="10" label="Alignment Range Start" />
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45 <param name="alirangeend" type="integer" value="20" label="Alignment Range End" />
0
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46 </repeat>
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47 </when>
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48 </conditional>
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49
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50 <!-- TODO: support model2ali/ali2model as separate utilities? -->
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51 <expand macro="format_selector"/>
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52 <expand macro="mcss"/>
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53 <expand macro="arsws"/>
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54 <expand macro="seed"/>
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55 </inputs>
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56 <outputs>
3
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57 <data name="output" format="stockholm" label="Output MSA"/>
0
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="msafile" value="globins4.sto"/>
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62 <param name="modelrangestart" value="10" />
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63 <param name="modelrangeend" value="20" />
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64 <expand macro="seed_test" />
5
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65 <output name="output" file="globins-masked.sto" lines_diff="4">
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66 <assert_contents>
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67 <has_line_matching expression="# STOCKHOLM.*"/>
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68 <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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69 </assert_contents>
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70 </output>
0
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 @HELP_PRE@
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75
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76 alimask is used to apply a mask line to a multiple sequence alignment, based on
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77 provided alignment or model coordinates. When hmmbuild receives a masked
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78 alignment as input, it produces a profile model in which the emission
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79 probabilities at masked positions are set to match the background frequency,
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80 rather than being set based on observed frequencies in the alignment.
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81 Position-specific insertion and deletion rates are not altered, even in masked
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82 regions. alimask autodetects input format, and produces masked alignments in
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83 Stockholm format. <msafile> may contain only one sequence alignment.
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84
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85 A common motivation for masking a region in an alignment is that the region
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86 contains a simple tandem repeat that is observed to cause an unacceptably high
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87 rate of false positive hits.
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88
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89 In the simplest case, a mask range is given in coordinates relative to the
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90 input alignment, using --alirange <s>. However it is more often the case that
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91 the region to be masked has been identified in coordinates relative to the
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92 profile model (e.g. based on recognizing a simple repeat pattern in false hit
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93 alignments or in the HMM logo). Not all alignment columns are converted to
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94 match state positions in the profile (see the --symfrac flag for hmmbuild for
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95 discussion), so model positions do not necessarily match up to alignment column
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96 positions. To remove the burden of converting model positions to alignment
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97 positions, alimask accepts the mask range input in model coordinates as well,
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98 using --modelrange <s>. When using this flag, alimask determines which
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99 alignment positions would be identified by hmmbuild as match states, a process
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100 that requires that all hmmbuild flags impacting that decision be supplied to
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101 alimask. It is for this reason that many of the hmmbuild flags are also used by
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102 alimask.
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103
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104 @HELP_PRE_OTH@
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105
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106 **Ranges**
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107
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108 Ranges are expressed as a hyphenated pair of integers, e.g. 12-40. Ranges can
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109 be expressed in terms of model coordinates or alignment coordinates.
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110
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111 @FORMAT_SELECTOR_HELP@
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112 @MCSS_HELP@
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113 @ARSWS_HELP@
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114 @SEED_HELP@
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115
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116 @ATTRIBUTION@
3
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117 ]]></help>
0
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118 <expand macro="citation"/>
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119 </tool>