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1 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0">
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2 <description>Rapidly align sequences to the genome</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 blat
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8 #if $noHead
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9 -noHead
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10 #end if
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11 -q=$query_type
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12 -t=$database_type
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13 -mask=$mask
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14 '${database}'
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15 '${query}'
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16 '${output}'
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17
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18 ]]></command>
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19 <inputs>
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20 <param type="data" name="database" format="fasta" />
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21 <param type="data" name="query" format="fasta" />
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22 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dna">
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23 <option value="dna">DNA sequence</option>
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24 <option value="prot">protein sequence</option>
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25 <option value="dnax">DNA sequence translated in six frames to protein</option>
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26 </param>
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27 <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is dna">
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28 <option value="dna">DNA sequence</option>
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29 <option value="rna">RNA sequence</option>
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30 <option value="prot">protein sequence</option>
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31 <option value="dnax">DNA sequence translated in six frames to protein</option>
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32 <option value="rnax">DNA sequence translated in three frames to protein</option>
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33 </param>
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34 <param name="noHead" type="boolean" value="false" label="Suppresses .psl header (so it's just a tab-separated file)." />
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35 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
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36 but may extend through it in nucleotide searches. Masked areas
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37 are ignored entirely in protein or translated searches.">
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38 <option value="lower">lower - mask out lower-cased sequence</option>
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39 <option value="upper">upper - mask out upper-cased sequence</option>
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40 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
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41 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
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42 </param>
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43 <!--<conditional name="database" format="fasta">
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44 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dna">
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45 <option value="dna">DNA sequence</option>
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46 <option value="prot">protein sequence</option>
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47 <option value="dnax">DNA sequence translated in six frames to protein</option>
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48 </param>
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49 <when value="dna">
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50 <param type="integer" name="tileSize" value="11" min="1" max="12" label="tileSize" help="Sets the size of match that triggers an alignment. Usually between 8 and 12">tileSize</param>
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51 <param name="minMatch" type="integer" value="2" label="Sets the number of tile matches. Usually set from 2 to 4.
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52 Default is 2 for nucleotide, 1 for protein.">-minMatch</param>
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53 <param name="minIdentity" type="integer" value="90" label="Sets minimum sequence identity (in percent). Default is
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54 90 for nucleotide searches, 25 for protein or translated
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55 protein searches.">-minIdentity</param>
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56
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57 </when>
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58 <when value="prot">
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59 <param type="integer" name="tileSize" value="5" min="1" max="12" label="tileSize" help="Sets the size of match that triggers an alignment. Usually between 8 and 12">tileSize</param>
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60 <param name="minMatch" type="integer" value="1" label="Sets the number of tile matches. Usually set from 2 to 4.
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61 Default is 2 for nucleotide, 1 for protein.">-minMatch</param>
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62 <param name="minIdentity" type="integer" value="25" label="Sets minimum sequence identity (in percent). Default is
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63 90 for nucleotide searches, 25 for protein or translated
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64 protein searches.">-minIdentity</param>
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65 </when>
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66 </conditional>
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67 <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is dna">
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68 <option value="dna">DNA sequence</option>
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69 <option value="rna">RNA sequence</option>
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70 <option value="prot">protein sequence</option>
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71 <option value="dnax">DNA sequence translated in six frames to protein</option>
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72 <option value="rnax">DNA sequence translated in three frames to protein</option>
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73 </param>
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74 <conditional name="settings">
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75 <param name="advanced" type="select" multiple="false" label="Specify advanced parameters">
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76 <option value="simple" selected="true">No, use program defaults. </option>
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77 <option value="advanced">Yes, see full parameter list.</option>
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78 </param>
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79 <when value="advanced">
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80 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
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81 but may extend through it in nucleotide searches. Masked areas
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82 are ignored entirely in protein or translated searches.">
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83 <option value="lower">lower - mask out lower-cased sequence</option>
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84 <option value="upper">upper - mask out upper-cased sequence</option>
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85 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
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86 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
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87 </param>
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88 <param name="qmask" type="select" label="Mask out repeats in query sequence" help="Similar to -mask above, but
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89 for query rather than target sequence.">
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90 <option value="lower">lower - mask out lower-cased sequence</option>
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91 <option value="upper">upper - mask out upper-cased sequence</option>
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92 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
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93 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
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94 </param>
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95 <param name="oneOff" type="integer" value="0" label="If set to 1, this allows one mismatch in tile and still triggers an alignment. Default is 0.">-oneOff</param>
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96 <param name="minScore" type="integer" value="30" label="Sets minimum score. This is the matches minus the
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97 mismatches minus some sort of gap penalty. Default is 30.">-minScore</param>
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98 <param name="maxGap" type="integer" value="2" label="Sets the size of maximum gap between tiles in a clump. Usually
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99 set from 0 to 3. Default is 2. Only relevent for minMatch > 1.">-maxGap</param>
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100 <param name="minRepDivergence" type="integer" value="15" min="0" max="100" label="Minimum percent divergence of repeats to allow
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101 them to be unmasked. Default is 15. Only relevant for
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102 masking using RepeatMasker .out files.">-minRepDivergence</param>
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103 <param name="noHead" type="boolean" value="false" label="Suppresses .psl header (so it's just a tab-separated file)." />
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104 <param name="dots" type="integer" value="0" label="Output dot every N sequences to show program's progress." />
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105 <param name="trimT" type="boolean" value="false" label="Trim leading poly-T." />
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106 <param name="trimHardA" type="boolean" value="false" label="Remove poly-A tail from qSize as well as alignments in
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107 psl output." />
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108 <param name="fastMap" type="boolean" value="false" label="Run for fast DNA/DNA remapping - not allowing introns,
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109 requiring high %ID. Query sizes must not exceed 5000." />
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110 <param name="fine" type="boolean" value="false" label="For high-quality mRNAs, look harder for small initial and
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111 terminal exons. Not recommended for ESTs." />
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112 <param name="out" type="select" label="Output file format">
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113 <option value="psl" selected="true">psl - Default. Tab-separated format, no sequence</option>
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114 <option value="pslx">pslx - Tab-separated format with sequence</option>
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115 <option value="axt">axt - blastz-associated axt format</option>
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116 <option value="maf">maf - multiz-associated maf format</option>
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117 <option value="sim4">sim4 - similar to sim4 format</option>
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118 <option value="wublast">wublast - similar to wublast format</option>
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119 <option value="blast">blast - similar to NCBI blast format</option>
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120 <option value="blast8">blast8- NCBI blast tabular format</option>
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121 <option value="blast9">blast9 - NCBI blast tabular format with comments</option>
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122 </param>
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123 <param name="maxIntro" type="integer" value="750000" label="Sets maximum intron size. Default is 750000." />
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124 <param name="extendThroughN" type="boolean" value="false" label="Allows extension of alignment through large blocks of Ns." />
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125 </when>
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126 </conditional>-->
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127 </inputs>
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128 <outputs>
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129 <data format="psl" name="output"></data>
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130 </outputs>
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131 <tests>
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132 <test>
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133 <param name="database" value="amaVit1.fa" />
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134 <param name="query" value="Gallus_gallus_RefSeq.fa" />
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135 <param name="database_type" value="dnax" />
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136 <param name="query_type" value="rnax" />
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137 <param name="noHead" value="true" />
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138 <param name="mask" value="lower" />
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139 <output name="output" value="amaVit1_Gallus_gallus.psl" />
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140 </test>
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141 </tests>
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142 </tool>
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