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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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1
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23 <tests>
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24 <test>
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25 <param name="iupac" value="WGATAR" />
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26 <param name="fasta" value="phix.fa" />
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27 <param name="label" value="IUPAC_or_name" />
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28 <param name="strand" value="0" />
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29 <output name="output" file="iupac_each_match.gff" />
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30 </test>
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31 </tests>
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32
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33 <help>
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34 .. class:: infomark
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35
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36 **What it does**
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37
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38 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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39
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40 IUPAC = Nucleotide(s):
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41
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42 A = A
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43
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44 C = C
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45
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46 G = G
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47
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48 T = T
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49
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50 M = A/C
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51
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52 R = A/G
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53
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54 W = A/T
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55
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56 S = C/G
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57
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58 Y = C/T
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59
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60 K = G/T
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61
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62 V = A/C/G
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63
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64 H = A/C/T
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65
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66 D = A/G/T
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67
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68 B = C/G/T
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69
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70 N = A/C/G/T
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71
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72 ----
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73
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74 .. class:: infomark
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75
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76 **Options**
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77
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78 '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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79
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80 '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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81
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82 '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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83
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84 ----
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85
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86 .. class:: infomark
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87
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88 **Credits**
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89
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90 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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91
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92 Please kindly acknowledge both this Galaxy tool and Scan_IUPAC_output_each_match.pl if you use it.
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93 </help>
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94
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95 </tool>
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96
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