Mercurial > repos > iuc > hmmer_hmmemit

annotate hmmemit.xml @ 8:e9d622609fb5 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 20:24:12 +0000
parents 9415f29a3926
children be03abdc6451
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f48f9bbfcfd8 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_hmmemit" name="hmmemit" version="@TOOL_VERSION@">
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e9d622609fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 061757dd7b3bfe66b7738fd54bd6c5e135d9afe8
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3 <description>sample sequence(s) from a profile HMM</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 hmmemit
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12
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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13 #if $oformat.oformat_select == "fasta":
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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14 -N $oformat.N_fa
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15 #elif $oformat.oformat_select == "aln":
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16 -N $oformat.N_aln
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17 -a
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18 #elif $oformat.oformat_select == "mrcs":
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19 -c
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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20 #elif $oformat.oformat_select == "mrcsf":
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21 --minl $oformat.minl
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22 --minu $oformat.minu
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23 -C
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24 #else:
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25 -N $oformat.N_smp
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26 -p
3
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27 #if str($oformat.L):
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28 -L $oformat.L
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29 #end if
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30 $oformat.emission_profiles
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31 #end if
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32
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33 @SEED@
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34
3
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35 '$hmmfile'
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36 > '$output'
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37 ]]></command>
0
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38 <inputs>
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39 <expand macro="input_hmm" />
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40
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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41 <conditional name="oformat">
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42 <param name="oformat_select" type="select" label="Output Format">
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43 <option value="fasta" selected="true">Fasta</option>
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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44 <option value="aln">Alignment</option>
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45 <option value="mrcs">Majority-Rule Concensus Sequence</option>
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46 <option value="mrcsf">Fancier Concensus Sequence</option>
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47 <option value="sample">Sample sequences from profile, not core model</option>
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48 </param>
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49 <when value="fasta">
3
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50 <param name="N_fa" argument="-N" type="integer" min="1" value="1"
0
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51 label="Number of sequences to generate"/>
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52 </when>
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53 <when value="aln">
3
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54 <param name="N_aln" argument="-N" type="integer" min="1" value="1"
0
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55 label="Number of sequences to generate"/>
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56 </when>
3
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57 <when value="mrcs" />
0
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58 <when value="mrcsf">
3
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59 <param argument="--minl" type="float" value="0.7"
0
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60 label="show consensus as 'any' (X/N) unless >= this fraction"/>
3
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61 <param argument="--minu" type="float" value="0.2"
0
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62 label="show consensus as upper case if >= this fraction"/>
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63 </when>
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64 <when value="sample">
3
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65 <param name="N_smp" argument="-N" type="integer" min="1" value="1"
0
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66 label="Number of sequences to generate"/>
3
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67 <param argument="-L" type="integer" optional="true"
0
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68 label="Expected length of profile"/>
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69
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70 <param name="emission_profiles" type="select" label="Emission profile options">
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71 <option value="--local" selected="true">configure profile in multihit local mode</option>
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72 <option value="--unilocal">configure profile in unilocal mode</option>
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73 <option value="--glocal">configure profile in multihit glocal mode</option>
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74 <option value="--uniglocal">configure profile in unihit glocal mode</option>
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75 </param>
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76 </when>
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77 </conditional>
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78
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79 <expand macro="seed"/>
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80 </inputs>
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81 <outputs>
3
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82 <data name="output" format="fasta" label="Sequences generated from $hmmfile.name">
0
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83 <change_format>
5
9415f29a3926 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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84 <when input="oformat.oformat_select" value="aln" format="stockholm"/>
0
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85 <!-- the rest are fasta -->
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86 </change_format>
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87 </data>
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88 </outputs>
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89 <tests>
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90 <test>
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91 <param name="hmmfile" value="globins4.hmm"/>
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92 <param name="oformat_select" value="aln"/>
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93 <param name="N_aln" value="10"/>
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94 <expand macro="seed_test" />
5
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95 <output name="output" file="globins4-emit.sto" ftype="stockholm" compare="sim_size">
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96 <assert_contents>
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97 <has_line_matching expression="# STOCKHOLM.*"/>
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98 <has_line_matching expression="//"/>
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99 </assert_contents>
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100 </output>
0
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101 </test>
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102 <test>
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103 <param name="hmmfile" value="globins4.hmm"/>
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104 <param name="oformat_select" value="fasta"/>
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105 <param name="N_aln" value="10"/>
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106 <expand macro="seed_test" />
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107 <output name="output" file="globins4-emit-1.sto" ftype="fasta" compare="sim_size">
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108 <assert_contents>
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109 <has_line_matching expression=">.*"/>
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110 </assert_contents>
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111 </output>
0
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112 </test>
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113 </tests>
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114 <help><![CDATA[
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115 @HELP_PRE@
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116
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117 The hmmemit program samples (emits) sequences from the profile HMM(s) in
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118 hmmfile, and writes them to output. Sampling sequences may be useful for a
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119 variety of purposes, including creating synthetic true positives for benchmarks
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120 or tests.
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121
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122 The default is to sample one unaligned sequence from the core probability
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123 model, which means that each sequence consists of one full-length domain.
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124 Alternatively, with the -c option, you can emit a simple majority-rule
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125 consensus sequence; or with the -a option, you can emit an alignment (in which
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126 case, you probably also want to set -N to something other than its default of 1
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127 sequence per model).
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128
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129 As another option, with the -p option you can sample a sequence from a fully
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130 configured HMMER search profile. This means sampling a ‘homologous sequence’ by
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131 HMMER’s definition, including nonhomologous flanking sequences, local
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132 alignments, and multiple domains per sequence, depending on the length model
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133 and alignment mode chosen for the profile.
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134
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135 The hmmfile may contain a library of HMMs, in which case each HMM will be used
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136 in turn.
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137
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138 @HELP_PRE_OTH@
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139
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140 Output Formats
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141 --------------
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142
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143 Several output formats are available, each with different options.
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144
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145 **Fasta**
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146
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147 Fasta option is the easiest to understand, given an input model, it will produce N sequences in fasta format from that model.
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148
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149 **Alignment**
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150
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151 Produces a stockholm alignment, of what the Fasta output would have produced.
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152
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153 **Majority-Rule Concensus Sequence**
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154
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155 Emit a plurality-rule consensus sequence, instead of sampling a sequence from
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156 the profile HMM’s probability distribution. The consensus sequence is formed by
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157 selecting the maximum probability residue at each match state.
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158
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159 **Fancier Concensus Sequence**
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160
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161 Emit a fancier plurality-rule consensus sequence than the -c option. If the
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162 maximum probability residue has p < minl show it as a lower case ’any’ residue
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163 (n or x); if p >= minl and < minu show it as a lower case residue; and if p >=
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164 minu show it as an upper case residue. The default settings of minu and minl
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165 are both 0.0, which means -C gives the same output as -c unless you also set
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166 minu and minl to what you want.
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167
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168 **Sample**
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169
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170 Sample unaligned sequences from the implicit search profile, not from the core
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171 model. The core model consists only of the homologous states (between the begin
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172 and end states of a HMMER Plan7 model). The profile includes the nonhomologous
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173 N, C, and J states, local/glocal and uni/multihit algorithm configuration, and
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174 the target length model. Therefore sequences sampled from a profile may in-
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175 clude nonhomologous as well as homologous sequences, and may contain more than
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176 one homologous sequence segment. By default, the profile is in multihit local
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177 mode, and the target sequence length is configured for L=400.
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178
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179 @ATTRIBUTION@
3
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180 ]]></help>
0
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181 <expand macro="citation"/>
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182 </tool>