Mercurial > repos > yating-l > ucsc_blat

annotate blat.xml @ 26:7e37f4933132 draft

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planemo upload commit 630d4a316c3b72b0d92b32e8b37303d247a41190
author iuc
date Thu, 31 May 2018 11:25:20 -0400
parents 3ce3e446f081
children f90551569666
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1 <?xml version="1.0"?>
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2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="36">
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3 <description>BLAST-like sequence alignment tool</description>
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4 <requirements>
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5 <requirement type="package" version="36">blat</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if str($reference_source.reference_source_selector) == "history":
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9 ## blat depends on file extension
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10 #if $reference_source.database.is_of_type("fasta"):
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11 #set $reference_fasta_filename = "localref.fa"
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12 #elif $reference_source.database.is_of_type("twobit"):
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13 #set $reference_fasta_filename = "localref.2bit"
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14 #else
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15 #set $reference_fasta_filename = "localref"
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16 #end if
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17
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18 ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
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19 #else:
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20 #set $reference_fasta_filename = str($reference_source.database.fields.path)
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21 #end if
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23 blat
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24
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25 -q=$query_type
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26 -t=$database_type
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27
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28 ${oneOff}
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29
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30 #if str($minScore)
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31 -minScore=${minScore}
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32 #end if
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33
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34 -maxGap=${maxGap}
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35
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36 #if str($repMatch)
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37 -repMatch=${repMatch}
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38 #end if
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39
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40 #if $mask_type.mask == "file.out":
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41 -mask='${mask_type.mask_file}'
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42 #else:
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43 -mask=$mask_type.mask
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44 #end if
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45
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46 #if str($dots)
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47 -dots=${dots}
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48 #end if
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49
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50 ${trimT}
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51 ${noTrimA}
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52 ${trimHardA}
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53 ${fastMap}
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54 ${fine}
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55
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56 #if str($maxIntron)
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57 -maxIntron=${maxIntron}
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58 #end if
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59
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60 ${extendThroughN}
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61
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62 '$reference_fasta_filename'
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63 '${query}'
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64
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65 -out=${out}
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66
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67 '${output}'
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68 ]]></command>
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69 <inputs>
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70 <conditional name="reference_source">
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71 <param name="reference_source_selector" type="select" label="Choose the source for the database">
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72 <option value="cached">Locally cached</option>
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73 <option value="history">History</option>
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74 </param>
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75 <when value="cached">
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76 <param name="database" type="select" label="Select database">
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77 <options from_data_table="all_fasta">
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78 <filter type="sort_by" column="2" />
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79 </options>
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80 <validator type="no_options" message="A built-in database is not available" />
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81 </param>
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82 </when>
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83 <when value="history">
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84 <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" />
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85 </when>
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86 </conditional>
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87 <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/>
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88 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t">
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89 <option value="dna">dna - DNA sequence</option>
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90 <option value="prot">prot - protein sequence</option>
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91 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
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92 </param>
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93 <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is rnax" argument="-q">
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94 <option value="dna">dna - DNA sequence </option>
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95 <option value="rna">rna - RNA sequence</option>
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96 <option value="prot">prot - protein sequence</option>
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97 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
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98 <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option>
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99 </param>
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100 <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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101 <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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102 <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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103 <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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104 <conditional name="mask_type">
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105 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
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106 but may extend through it in nucleotide searches. Masked areas
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107 are ignored entirely in protein or translated searches. Default is lower" argument="-mask">
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108 <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
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109 <option value="upper">upper - mask out upper-cased sequence</option>
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110 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
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111 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
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112 </param>
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113 <when value="lower" />
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114 <when value="upper" />
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115 <when value="out" />
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116 <when value="file.out">
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117 <param name="mask_file" type="data" format="txt" label="RepeatMasker file.out" />
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118 </when>
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119 </conditional>
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120 <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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121 <param argument="-trimT" type="boolean" truevalue="-trimT" falsevalue="" label="Trim leading poly-T" />
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122 <param argument="-noTrimA" type="boolean" truevalue="-noTrimA" falsevalue="" label="Don't trim trailing poly-A" />
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123 <param argument="-trimHardA" type="boolean" truevalue="-trimHardA" falsevalue="" label="Remove poly-A tail from qSize and alignments in .psl output" />
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124 <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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125 <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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126 <param argument="-maxIntron" type="integer" value="750000" optional="true" label="Maximum intron size" />
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127 <param argument="-extendThroughN" type="boolean" truevalue="-extendThroughN" falsevalue="" label="Allow extension of alignment through large blocks of N's" />
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128 <param name="out" type="select" label="Select output file format (-out)">
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129 <option value="psl">Tab-separated format, no sequence (psl)</option>
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130 <option value="psl -noHead">Tab-separated format, no sequence, no header (psl -noHead)</option>
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131 <option value="axt">Blastz-associated axt format (axt)</option>
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132 <option value="maf">Multiz-associated maf format (maf)</option>
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133 <option value="sim4">Similar to sim4 format (sim4)</option>
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134 <option value="wublast">Similar to WU-BLAST format (wublast)</option>
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135 <option value="blast">Similar to NCBI BLAST format (blast)</option>
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136 <option value="blast8">NCBI BLAST tabular format (blast8)</option>
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137 <option value="blast9">NCBI BLAST tabular format with comments (blast9)</option>
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138 </param>
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139 </inputs>
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140 <outputs>
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141 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
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142 <change_format>
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143 <when input="out" value="psl" format="psl" />
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144 <when input="out" value="axt" format="axt" />
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145 <when input="out" value="maf" format="maf" />
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146 <when input="out" value="sim4" format="txt" />
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147 <when input="out" value="wublast" format="txt" />
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148 <when input="out" value="blast" format="txt" />
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149 </change_format>
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150 </data>
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151 </outputs>
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152 <tests>
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153 <!-- test on query of GenBank RefSeq records for Gallus gallus and database of Amazona vittata -->
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154 <test>
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155 <param name="reference_source_selector" value="history" />
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156 <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
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157 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
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158 <param name="database_type" value="dnax" />
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159 <param name="query_type" value="rnax" />
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160 <param name="mask" value="lower" />
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161 <param name="out" value="psl -noHead" />
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162 <output name="output" value="amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl" sort="True"/>
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163 </test>
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164 <!-- test on query of partial mRNA of Drosophila melanogaster and the database of Drosophila biamipes dot chromosome -->
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165 <test>
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166 <param name="reference_source_selector" value="history" />
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167 <param name="database" value="dbia3/dbia3.fa" />
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168 <param name="query" value="dbia3/dmel-transcript.fa" />
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169 <param name="database_type" value="dnax" />
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170 <param name="query_type" value="rnax" />
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171 <param name="mask" value="lower" />
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172 <param name="out" value="psl -noHead" />
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173 <param name="maxIntron" value="" />
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174 <output name="output" value="dbia3/dbia3.sorted.psl" sort="True"/>
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175 </test>
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176 <!-- test on the database masked by repeat masker -->
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177 <test>
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178 <param name="reference_source_selector" value="history" />
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179 <param name="database" value="dbia3/dbia3_masked.2bit" />
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180 <param name="query" value="dbia3/dmel-transcript.fa" />
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181 <param name="database_type" value="dnax" />
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182 <param name="query_type" value="rnax" />
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183 <param name="oneOff" value="false" />
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184 <param name="minScore" value="30" />
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185 <param name="maxGap" value="2" />
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186 <param name="trimT" value="false" />
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187 <param name="noTrimA" value="false" />
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188 <param name="fine" value="false" />
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189 <param name="maxIntron" value="750000" />
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190 <param name="extendThroughN" value="false" />
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191 <param name="mask" value="file.out" />
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192 <param name="mask_file" value="dbia3/dbia3_RM.out" />
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193 <param name="out" value="psl -noHead" />
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194 <output name="output" value="dbia3/dbia3_masked.sorted.psl"/>
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195 </test>
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196
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197 </tests>
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198 <help>
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199 <![CDATA[
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200 BLAT
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201 ====
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202 BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.
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203
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204 blat (version: v36)- Standalone blat sequence search command line tool.
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205 -------------------------------------------------------------------------
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206
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207 usage:
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208 ++++++
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209
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210 $ blat database query [-ooc=11.ooc] output.psl
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211
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212 where:
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213 database and query are each either a .fa, .nib or .2bit file,
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214 or a list of these files with one file name per line.
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215 -ooc=11.ooc tells the program to load over-occurring 11-mers from
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216 an external file. This will increase the speed
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217 by a factor of 40 in many cases, but is not required.
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218 output.psl is the name of the output file.
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219
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220 documentation:
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221 ++++++++++++++
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222
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223 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
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224
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225 Source code:
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226 ++++++++++++
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227
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228 http://hgdownload.cse.ucsc.edu/admin/exe/
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229
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230 ]]></help>
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231 <citations>
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232 <citation type="doi">10.1101/gr.229202</citation>
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233 </citations>
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234 </tool>