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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="fasta_scan_iupac_each" name="IUPAC scan and output each match" version="@VERSION@">
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3 <description>Returns all matches to a given IUPAC in GFF format</description>
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4 <macros>
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5 <import>motif_tools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command><![CDATA[
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9 perl $__tool_directory__/Scan_IUPAC_output_each_match.pl $iupac $fasta $output $label $strand
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10 ]]></command>
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11 <inputs>
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12 <param name="iupac" type="text" label="IUPAC string" value="e.g. WGATAR" help="Enter an IUPAC string." size="20"/>
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13 <param format="fasta" name="fasta" type="data" label="FASTA file" help="Select a FASTA file containing the sequences to be scanned."/>
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14 <param name="label" type="text" label="Attribute in GFF output" value="IUPAC_or_name" help="The label will be included at the end (attibute) section of each GFF line. This could be the IUPAC string used or the name of the motif." size="20"/>
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15 <param name="strand" type="select" label="Select sequence strands to scan" help="Scan either both strands or only the forward strand.">
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16 <option value="0">Scan both strands</option>
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17 <option value="1">Only scan forward strand</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="gff" name="output" />
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22 </outputs>
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23
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24 <help>
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25 .. class:: infomark
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26
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27 **What it does**
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28
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29 This tool will find all matches to a DNA pattern in the input DNA sequence, represented by an IUPAC string. The matches are non-overlapping, so searching with 'TTTT' in 'TTTTTTTT' will find two hits to the IUPAC. The output is in GFF format and the last 'attribute' field can be specified using the 'Label' option.
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30
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31 IUPAC = Nucleotide(s):
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32
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33 A = A
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34
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35 C = C
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36
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37 G = G
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38
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39 T = T
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40
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41 M = A/C
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42
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43 R = A/G
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44
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45 W = A/T
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46
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47 S = C/G
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48
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49 Y = C/T
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50
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51 K = G/T
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52
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53 V = A/C/G
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54
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55 H = A/C/T
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56
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57 D = A/G/T
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58
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59 B = C/G/T
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60
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61 N = A/C/G/T
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62
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63 ----
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64
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65 .. class:: infomark
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66
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67 **Options**
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68
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69 'IUPAC string' - can be entered as upper- or lower-case as the tool will force them to become upper-case, but will only accept the IUPAC codes listed above.
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70
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71 'Attribute in GFF output' - the last field of each GFF line 'attribute' can be specified using the 'Label' option, this should only include letters/numbers, but without spaces.
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72
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73 'Select sequence strands to scan' - Only scanning the forward strand of the input sequence is useful if the IUPAC is a palindrome (e.g. CANNTG).
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74
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75 ----
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76
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77 .. class:: infomark
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78
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79 **Credits**
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80
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81 This Galaxy tool has been developed within the Bioinformatics Core Facility at the University of Manchester. It runs the Scan_IUPAC_output_each_match.pl Perl script that was written by Ian Donaldson.
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82
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83 Please kindly acknowledge both this Galaxy tool and Scan_IUPAC_output_each_match.pl if you use it.
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84 </help>
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85
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86 </tool>
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87
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