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1 <tool id="blat_wrapper" name="BLAT" version="1.0.0">
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2 <description> compare sequencing reads against UCSC genome builds</description>
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3 <command interpreter="python">
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4 #if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
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5 #else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
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6 #end if# ${GALAXY_DATA_INDEX_DIR}
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7 </command>
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8 <inputs>
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9 <conditional name="source">
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10 <param name="source_select" type="select" label="Target source">
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11 <option value="database">Genome Build</option>
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12 <option value="input_ref">Your Upload File</option>
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13 </param>
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14 <when value="database">
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15 <param name="dbkey" type="genomebuild" label="Genome" />
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16 </when>
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17 <when value="input_ref">
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18 <param name="input_target" type="data" format="fasta" label="Reference sequence" />
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19 </when>
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20 </conditional>
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21 <param name="input_query" type="data" format="fasta" label="Sequence file"/>
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22 <param name="iden" type="float" size="15" value="90.0" label="Minimal identity (-minIdentity)" />
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23 <param name="tile_size" type="integer" size="15" value="11" label="Minimal size of exact match (-tileSize)" help="Must be between 6 and 18."/>
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24 <param name="one_off" type="integer" size="15" value="0" label="Number of mismatch in the word (-oneOff)" help="Must be between 0 and 2." />
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25 </inputs>
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26 <outputs>
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27 <data name="output1" format="tabular"/>
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28 </outputs>
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29 <requirements>
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30 <requirement type="binary">blat</requirement>
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31 </requirements>
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32 <tests>
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33 <test>
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34 <param name="source_select" value="database" />
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35 <param name="dbkey" value="eschColi_K12" />
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36 <param name="input_query" value="blat_wrapper_test1.fa" ftype="fasta"/>
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37 <param name="iden" value="90.0" />
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38 <param name="tile_size" value="11" />
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39 <param name="one_off" value="0" />
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40 <output name="output1" file="blat_wrapper_test1.out" />
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41 </test>
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42 </tests>
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43 <help>
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44
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45 .. class:: warningmark
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46
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47 Using a smaller word size (*Minimal Size of Exact Match*) will increase the computational time.
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48
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49 .. class:: warningmark
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50
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51 Using a larger mismatch number (*Number of Mismatch in the Word*) will increase the computational time.
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52
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53 -----
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54
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55 **What it does**
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56
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57 This tool currently uses the **BLAT** alignment program. Your short reads file is searched against a genome build or another uploaded file.
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58
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59 -----
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60
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61 **Example**
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62
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63 - Input a multiple fasta file::
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64
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65 >seq1
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66 TGGTAATGGTGGTTTTTTTTTTTTTTTTTTATTTTT
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67
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68 - Use the default settings:
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69
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70 - alignment identity must be higher than or equal to 90%.
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71
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72 - minimal size of exact match to trigger an alignment is 11.
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73
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74 - allow 0 mismatches in the above exact match size.
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75
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76 - Search against ce2 (C. elegans March 2004), partial result::
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77
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78 25 1 0 0 0 0 0 0 + seq1 36 10 36 chrI 15080483 9704438 9704464 1 26, 10, 9704438, ggttttttttttttttttttattttt, ggtttttttttttttttttttttttt,
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79 27 0 0 0 0 0 1 32 + seq1 36 9 36 chrI 15080483 1302536 1302595 2 21,6, 9,30, 1302536,1302589, tggtttttttttttttttttt,attttt, tggtttttttttttttttttt,attttt,
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80
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81 -----
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82
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83 **Parameters**
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84
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85 - *Minimal Identity* (**-minIdentity**) : In percent, the minimum sequence identity between the query and target alignment. Default is 90.
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86
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87 - *Minimal Size of Exact Match* (**-tileSize**) : The size of a match that will trigger an alignment. Default is 11. Usually between 8 and 12. Must be between 6 and 18.
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88
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89 - *Number of Mismatch in the Word* (**-oneOff**) : The number of mismatches allowed in the word (tile size) and still triggers an alignment. Default is 0.
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90
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91 -----
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92
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93 **Reference**
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94
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95 **BLAT**: Kent, W James, BLAT--the BLAST-like alignment tool. (2002) Genome Research:12(4) 656-664.
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96
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97
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98 </help>
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99 </tool>
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