Mercurial > repos > yating-l > ucsc_blat

annotate blat.xml @ 13:820f68ad34a7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ commit f38778f3a25020809c3f6cf17aafb8dbfc54b2e8
author iuc
date Sat, 28 Sep 2024 16:29:35 +0000
parents e79965d0351c
children b8fa39b09aa4
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1 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>BLAST-like sequence alignment tool</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">469</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6
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7 <xml name="mask_cond" tokens="maskarg,label,help">
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8 <conditional name="@MASKARG@_type">
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9 <param argument="-@MASKARG@" type="select" label="@LABEL@" help="@HELP@">
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10 <option value="" selected="true">No masking</option>
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11 <option value="lower">lower - mask out lower-cased sequence</option>
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12 <option value="upper">upper - mask out upper-cased sequence</option>
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13 <option value="file.out">out - mask database according to RepeatMasker out</option>
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14 </param>
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15 <when value="" />
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16 <when value="lower" />
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17 <when value="upper" />
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18 <when value="file.out">
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19 <param name="@MASKARG@_file" type="data" format="txt" label="RepeatMasker file.out" />
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20 </when>
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21 </conditional>
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22 </xml>
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23 </macros>
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24 <xrefs>
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25 <xref type="bio.tools">blat</xref>
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26 </xrefs>
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27 <requirements>
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28 <requirement type="package" version="@TOOL_VERSION@">ucsc-blat</requirement>
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29 </requirements>
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30 <command detect_errors="exit_code"><![CDATA[
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31 #if str($reference_source.reference_source_selector) == "history":
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32 ## blat depends on file extension
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33 #if $reference_source.database.is_of_type("fasta.gz"):
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34 #set $reference_fasta_filename = "localref.fa.gz"
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35 #elif $reference_source.database.is_of_type("fasta"):
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36 #set $reference_fasta_filename = "localref.fa"
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37 #elif $reference_source.database.is_of_type("twobit"):
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38 #set $reference_fasta_filename = "localref.2bit"
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39 #else
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40 #set $reference_fasta_filename = "localref"
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41 #end if
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42 ln -s '$reference_source.database' '$reference_fasta_filename' &&
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43 #else:
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44 #set $reference_fasta_filename = str($reference_source.database.fields.path)
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45 #end if
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46
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47 ## blat depends on file extension
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48 #if $query.is_of_type("fasta.gz"):
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49 #set $query_filename = "query.fa.gz"
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50 #elif $query.is_of_type("fasta"):
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51 #set $query_filename = "query.fa"
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52 #elif $query.is_of_type("twobit"):
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53 #set $query_filename = "query.2bit"
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54 #else
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55 #set $query_filename = "query"
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56 #end if
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57 ln -s '$query' '$query_filename' &&
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58
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59 blat
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60 -q=$query_type
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61 -t=$database_type
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62 ## Basic alignment parameters
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63 #if str($basic_align.minScore)
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64 -minScore=$basic_align.minScore
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65 #end if
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66 #if str($basic_align.minIdentity)
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67 -minIdentity=$basic_align.minIdentity
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68 #end if
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69 $basic_align.trimT
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70 $basic_align.noTrimA
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71 $basic_align.trimHardA
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72 $basic_align.fastMap
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73 $basic_align.fine
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74 #if str($basic_align.maxIntron)
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75 -maxIntron=$basic_align.maxIntron
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76 #end if
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77 $basic_align.extendThroughN
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78 ## Advanced alignment parameters
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79 #if str($adv_align.tileSize)
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80 -tileSize=$adv_align.tileSize
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81 #end if
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82 #if str($adv_align.stepSize)
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83 -stepSize=$adv_align.stepSize
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84 #end if
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85 $adv_align.oneOff
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86 #if str($adv_align.minMatch)
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87 -minMatch=$adv_align.minMatch
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88 #end if
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89 -maxGap=$adv_align.maxGap
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90 #if str($adv_align.repMatch)
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91 -repMatch=$adv_align.repMatch
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92 #end if
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93 ## Repeat masking parameters
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94 #if $repeat.mask_type.mask == "file.out":
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95 -mask='$repeat.mask_type.mask_file'
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96 #elif $repeat.mask_type.mask:
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97 -mask=$repeat.mask_type.mask
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98 #end if
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99 #if $repeat.qMask_type.qMask == "file.out":
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100 -qMask='$repeat.qMask_type.qMask_file'
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101 #elif $repeat.qMask_type.qMask:
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102 -qmask=$repeat.qMask_type.qMask
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103 #end if
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104 #if $repeat.repeats_type.repeats == "file.out":
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105 -repeats='$repeat.repeats_type.repeats_file'
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106 #elif $repeat.repeats_type.repeats:
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107 -repeats=$repeat.repeats_type.repeats
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108 #end if
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109 #if str($repeat.minRepDivergence)
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110 -minRepDivergence=$repeat.minRepDivergence
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111 #end if
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112
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113 #if str($dots)
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114 -dots=$dots
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115 #end if
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116 '$reference_fasta_filename'
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117 '$query_filename'
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118 -out=$out
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119 '$output'
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120 ]]></command>
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121 <inputs>
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122 <conditional name="reference_source">
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123 <param name="reference_source_selector" type="select" label="Choose the source for the database">
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124 <option value="cached">Locally cached</option>
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125 <option value="history">History</option>
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126 </param>
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127 <when value="cached">
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128 <param name="database" type="select" label="Select database">
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129 <options from_data_table="all_fasta">
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130 <!-- <column name="name" index="0"/>
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131 <column name="value" index="2"/> -->
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132 <filter type="sort_by" column="2" />
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133 </options>
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134 <validator type="no_options" message="A built-in database is not available" />
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135 </param>
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136 </when>
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137 <when value="history">
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138 <param name="database" type="data" format="fasta,fasta.gz,twobit" label="Using database file, either a fasta, fasta.gz or twobit dataset" />
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139 </when>
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140 </conditional>
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141 <param name="query" type="data" format="fasta,fasta.gz,twobit" label="Query data, either a fasta, fasta.gz or twobit dataset"/>
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142 <param argument="-t" name="database_type" type="select" format="txt" multiple="false" label="database type" help="Choose your database type, the default is dnax">
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143 <option value="dna" selected="true">dna - DNA sequence</option>
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144 <option value="prot">prot - protein sequence</option>
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145 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
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146 </param>
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147 <param argument="-q" name="query_type" type="select" format="txt" multiple="false" label="query type" help="Choose your query type, the default is rnax">
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148 <option value="dna" selected="true">dna - DNA sequence </option>
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149 <option value="rna">rna - RNA sequence</option>
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150 <option value="prot">prot - protein sequence</option>
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151 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
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152 <option value="rnax">rnax - DNA sequence translated in three frames to protein</option>
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153 </param>
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154 <section name="basic_align" title="Alignment parameters" expanded="true">
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155 <param argument="-minScore" type="integer" value="30" label="Minimum score" help="It is the matches minus the mismatches minus some sort of gap penalty" />
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156 <param argument="-minIdentity" type="integer" value="" optional="true" min="0" max="100" label="Minimum sequence identity (in percent)" help="Default is 90 for nucleotide searches, 25 for protein or translated protein searches" />
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157 <param argument="-trimT" type="boolean" truevalue="-trimT" falsevalue="" label="Trim leading poly-T" />
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158 <param argument="-noTrimA" type="boolean" truevalue="-noTrimA" falsevalue="" label="Don't trim trailing poly-A" />
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159 <param argument="-trimHardA" type="boolean" truevalue="-trimHardA" falsevalue="" label="Remove poly-A tail from qSize and alignments in .psl output" />
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160 <param argument="-fastMap" type="boolean" truevalue="-fastMap" falsevalue="" label="Run for fast DNA/DNA remapping" help="It does not allow introns and require high %ID. Query sizes must not exceed 5000" />
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161 <param argument="-fine" type="boolean" truevalue="-fine" falsevalue="" label="Refine search for small initial and terminal exons" help="For high-quality mRNAs. Not recommended for ESTs" />
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162 <param argument="-maxIntron" type="integer" value="750000" optional="true" label="Maximum intron size" />
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163 <param argument="-extendThroughN" type="boolean" truevalue="-extendThroughN" falsevalue="" label="Allow extension of alignment through large blocks of N's" />
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164 </section>
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165 <section name="adv_align" title="Advanced alignment parameters" expanded="false">
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166 <param argument="-tileSize" type="integer" value="" optional="true" min="1" label="Tile size" help="Sets the size of match that triggers an alignment. Usually between 8 and 12. Default is 11 for DNA and 5 for protein" />
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167 <param argument="-stepSize" type="integer" value="" optional="true" min="1" label="Spacing between tiles" help="Default is tileSize" />
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168 <param argument="-oneOff" type="boolean" truevalue="-oneOff=1" falsevalue="" label="If set, this allows one mismatch in tile and still triggers an alignments" />
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169 <param argument="-minMatch" type="integer" value="" optional="true" min="1" label="Minimum number of tile matches" help="Usually set from 2 to 4. Default is 2 for nucleotide, 1 for protein." />
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170 <param argument="-maxGap" type="integer" value="2" min="0" max="3" label="Maximum gap between tiles in a clump" help="Usually set from 0 to 3. Only relevant for minMatch > 1" />
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171 <param argument="-repMatch" type="integer" value="" optional="true" label="Number of repetitions of a tile allowed before it is marked as overused" help="Typically this is 256 for tileSize 12, 1024 for tileSize 11, 4096 for tileSize 10. Also affected by stepSize. When stepSize is halved repMatch is doubled to compensate" />
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172 </section>
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173 <section name="repeat" title="Repeat masking parameters" expanded="true">
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174 <expand macro="mask_cond" maskarg="mask" label="Mask out repeats" help="Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas are ignored entirely in protein or translated searches. Default is no masking"/>
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175 <expand macro="mask_cond" maskarg="qMask" label="Mask out repeats in query sequence" help="Analoguous to -mask, but for the query sequence"/>
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176 <expand macro="mask_cond" maskarg="repeats" label="Report matches in repeats separately" help="Repeat bases will not be masked in any way, but matches in repeat areas will be reported separately from matches in other areas in the output"/>
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177 <param argument="-minRepDivergence" type="integer" value="" min="0" max="100" optional="true" label="Minimum divergence of repeats (percent)" help="to allow them to be unmasked. Default is 15. Only relevant for masking using RepeatMasker .out files" />
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178 </section>
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179 <param argument="-dots" type="integer" value="" optional="true" label="Output a dot every N sequences in log" help="Dots show program's progress" />
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180 <param name="out" type="select" label="Select output file format (-out)">
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181 <option value="psl">Tab-separated format, no sequence (psl)</option>
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182 <option value="psl -noHead">Tab-separated format, no sequence, no header (psl -noHead)</option>
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183 <option value="pslx">Tab-separated format (pslx)</option>
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184 <option value="pslx -noHead">Tab-separated format, no header (pslx -noHead)</option>
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185 <option value="axt">Blastz-associated axt format (axt)</option>
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186 <option value="maf">Multiz-associated maf format (maf)</option>
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187 <option value="sim4">Similar to sim4 format (sim4)</option>
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188 <option value="wublast">Similar to WU-BLAST format (wublast)</option>
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189 <option value="blast">Similar to NCBI BLAST format (blast)</option>
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190 <option value="blast8">NCBI BLAST tabular format (blast8)</option>
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191 <option value="blast9">NCBI BLAST tabular format with comments (blast9)</option>
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192 </param>
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193 </inputs>
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194 <outputs>
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195 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
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196 <change_format><!-- add test -->
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197 <when input="out" value="axt" format="axt" />
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198 <when input="out" value="maf" format="maf" />
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199 <when input="out" value="sim4" format="txt" />
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200 </change_format>
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201 </data>
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202 </outputs>
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203 <tests>
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204 <!-- test on query of GenBank RefSeq records for Gallus gallus and database of Amazona vittata -->
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205 <test>
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206 <conditional name="reference_source">
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207 <param name="reference_source_selector" value="history" />
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208 <param name="database" value="amaVit1_Gallus/amaVit1.fa" ftype="fasta" />
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209 </conditional>
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210 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" ftype="fasta" />
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211 <param name="database_type" value="dnax" />
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212 <param name="query_type" value="rnax" />
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213 <conditional name="mask_type">
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214 <param name="mask" value="lower" />
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215 </conditional>
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216 <param name="out" value="maf" />
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217 <output name="output" value="amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.maf" ftype="maf"/>
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218 <assert_command>
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219 <has_text text="-tileSize=" negate="true"/>
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220 <has_text text="-stepSize=" negate="true"/>
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221 <has_text text="-mask=lower"/>
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222 </assert_command>
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223 </test>
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224 <!-- test on query of partial mRNA of Drosophila melanogaster and the
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225 database of Drosophila biamipes dot chromosome
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226 - also test cached reference -->
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227 <test>
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228 <conditional name="reference_source">
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229 <param name="reference_source_selector" value="cached"/>
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230 <param name="database" value="dbdia display name"/>
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231 </conditional>
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232 <param name="query" value="dbia3/dmel-transcript.fa" ftype="fasta" />
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233 <param name="database_type" value="dnax" />
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234 <param name="query_type" value="rnax" />
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235 <section name="basic_align">
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236 <param name="maxIntron" value="" />
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237 </section>
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238 <section name="adv_align">
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239 <param name="tileSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
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240 <param name="stepSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
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241 </section>
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242 <param name="out" value="psl -noHead" />
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243 <output name="output" value="dbia3/dbia3.sorted.psl" ftype="tabular" sort="true">
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244 <assert_contents>
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245 <has_n_columns n="21"/>
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246 </assert_contents>
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247 </output>
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248 <assert_command>
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249 <has_text text="-tileSize=5"/>
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250 <has_text text="-mask" negate="true"/>
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251 </assert_command>
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252 </test>
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253 <test>
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254 <conditional name="reference_source">
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255 <param name="reference_source_selector" value="cached"/>
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256 <param name="database" value="dbdia display name"/>
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257 </conditional>
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258 <param name="query" value="dbia3/dmel-transcript.fa" ftype="fasta" />
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259 <param name="database_type" value="dnax" />
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260 <param name="query_type" value="rnax" />
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261 <section name="basic_align">
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262 <param name="maxIntron" value="" />
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263 </section>
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264 <section name="adv_align">
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265 <param name="tileSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
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266 <param name="stepSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
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267 </section>
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268 <param name="out" value="pslx -noHead" />
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269 <output name="output" value="dbia3/dbia3.sorted.psl" ftype="tabular" sort="true" compare="contains">
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270 <assert_contents>
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271 <has_n_columns n="23"/>
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272 </assert_contents>
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273 </output>
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274 <assert_command>
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275 <has_text text="-tileSize=5"/>
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276 <has_text text="-mask" negate="true"/>
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277 </assert_command>
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278 </test>
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279 <!-- test on the database masked by repeat masker -->
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280 <test>
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281 <conditional name="reference_source">
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282 <param name="reference_source_selector" value="history" />
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283 <param name="database" value="dbia3/dbia3_masked.2bit" ftype="twobit" />
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284 </conditional>
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285 <param name="query" value="dbia3/dmel-transcript.fa" ftype="fasta"/>
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286 <param name="database_type" value="dnax" />
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287 <param name="query_type" value="rnax" />
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288 <param name="oneOff" value="false" />
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289 <param name="minScore" value="30" />
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290 <param name="maxGap" value="2" />
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291 <param name="trimT" value="false" />
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292 <param name="noTrimA" value="false" />
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293 <param name="fine" value="false" />
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294 <param name="maxIntron" value="750000" />
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295 <param name="extendThroughN" value="false" />
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296 <conditional name="mask_type">
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297 <param name="mask" value="file.out" />
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298 <param name="mask_file" value="dbia3/dbia3_RM.out" />
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299 </conditional>
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300 <param name="out" value="psl" ftype="tabular" />
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301 <output name="output" value="dbia3/dbia3_masked.sorted.psl"/>
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302 <assert_command>
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303 <has_text text="-tileSize=" negate="true"/>
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304 <has_text text="-stepSize=" negate="true"/>
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305 <has_text text="-mask='/"/>
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306 </assert_command>
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307 </test>
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308 <!-- tiny test data from https://davetang.org/muse/2012/05/15/using-blat/ -->
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309 <test>
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310 <conditional name="reference_source">
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311 <param name="reference_source_selector" value="history" />
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312 <param name="database" value="mini-db.fa.gz" ftype="fasta.gz" />
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313 </conditional>
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314 <param name="query" value="mini-query.fa.gz" ftype="fasta.gz"/>
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315 <param name="minScore" value="0" />
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316 <section name="adv_align">
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317 <param name="stepSize" value="1"/>
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318 </section>
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319 <param name="out" value="psl" ftype="tabular" />
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320 <output name="output">
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321 <assert_contents>
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322 <has_n_lines n="7"/>
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323 </assert_contents>
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324 </output>
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325 <assert_command>
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326 <has_text text="-minScore=0"/>
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327 <has_text text="-stepSize=1"/>
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328 </assert_command>
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329 </test> </tests>
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330 <help>
0
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331 <![CDATA[
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332 BLAT
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333 ====
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334 BLAT is a bioinformatics software a tool which performs rapid sequence alignments (mRNA/DNA and cross-species protein).
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335 It is designed to find sequences of high similarity and have a certain minimum length. With the default setting this is
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336
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337 - >95% similarity and a minimum length of 25 bases for nucleotide sequences
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338 - >80% similarity and a minimum lenth of 20 amino acids for proteins
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339
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340 More divergent or shorter sequence alignments may be missed.
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341 The algorithm works in two phases:
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342
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343 1. Search phase: find regions of probable homology using an index of the reference sequence
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344 2. Alignment phase: Detailed Alignment of the sequences in these regions
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345
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346 Search phase
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347 ++++++++++++
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348
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349 Builds an index of the reference containing the nonoverlapping K-mers and their
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350 positions (by default, can be changed using `-tileSize` and `-stepSize`). Hits,
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351 i.e. exactly matching k-mers in query and reference, are then found by looking
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352 up each overlapping K-mer of the query sequence. By enabling `-oneOff` the
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353 algorithm allows for a single substitition. Note that this increases the run
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354 time of this phase significantly.
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355
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356 The hits are then split into buckets of 64k (based on the database position)
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357 and sorted on the diagonal (database minus query positions). Hits within the
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358 gap limit form so called proto-clumps. Those are then sorted by database position
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359 and put into clumps if they are within the window limit (wrt database coordinate).
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360
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361 Clumps with less than the minimum number of hits are discarded (-minMatch) and
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362 those within 300 bases or 100 amino acids in the database are merged together.
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363 The resulting clumps define regions of the database which are homologous to the
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364 query sequence which are then aligned.
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365
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366 Alignment phase
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367 +++++++++++++++
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368
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369 The alignment is performed differently for nucleotide and
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370 aminoacid sequences.
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371
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372 **Alignment for nucleotide sequences**: A hit list (exactly matching k-mers) for
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373 the query and the homologous region of the database is generated. If necessary
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374 hits are mode unique by extending them until they are unique or have a maximum
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375 size. The hits are then extended maximally allowing no mismatches, and overlapping
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376 hits are merged.
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377 Subsequent (wrt query and reference) extended hits are then linked in an
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378 alignment. If there are gaps in query and reference, the algorithm recurses
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379 using a smaller value for k until no additional hits are found or gaps are
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380 smaller than 6 bases.
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381
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382 **Protein Alignments**: The hits from the search stage are extended into maximally
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383 scoring ungapped alignments (HSPs) (match cost 2 and mismatch cost 1). The HSPs
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384 are organized in a directed graph where an edge connect HSPs A and B if A starts
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385 before B wrt query and database coordinates. The weight of the edge is then
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386 defined as the score of B minus a gap penalty based on the distance between A
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387 and B (overlapping HSPs are treated differently, see Kent 2002). The maximal
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388 scoring alignment is then determined as the maximum weight path through the
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389 graph and the HSPs of this path are removed. This is repeated until no HSPs are
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390 left.
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391
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392 **Stitching and Filling In**:
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393 In order to find also alignments of genes scattered across multiple homologous
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394 regions that have been determined in the search phase a variation of the
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395 alignment algorithm for proteins is employed. For details see Kent 2002.
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396
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397 Documentation:
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398 ++++++++++++++
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399
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400 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
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401
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402 Source code:
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403 ++++++++++++
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404
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405 http://hgdownload.cse.ucsc.edu/admin/exe/
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406
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407 ]]></help>
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408 <citations>
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409 <citation type="doi">10.1101/gr.229202</citation>
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410 </citations>
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411 </tool>