Mercurial > repos > pjbriggs > motif_tools
comparison Scan_IUPAC_output_each_match.xml @ 0:b67ea47730d3 draft
Version 1.0.1.
author | pjbriggs |
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date | Wed, 21 Mar 2018 06:39:41 -0400 |
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-1:000000000000 | 0:b67ea47730d3 |
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1 <?xml version="1.0" encoding="utf-8"?> | |
2 <tool id="fasta_scan_iupac_each" name="IUPAC scan and output each match" version="@VERSION@"> | |
3 <description>Returns all matches to a given IUPAC in GFF format</description> | |
4 <macros> | |
5 <import>motif_tools_macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command><![CDATA[ | |
9 perl $__tool_directory__/Scan_IUPAC_output_each_match.pl $iupac $fasta $output $label $strand | |
10 ]]></command> | |
11 <inputs> | |
12 <param name="iupac" type="text" label="IUPAC string" value="e.g. WGATAR" help="Enter an IUPAC string." size="20"/> | |
13 <param format="fasta" name="fasta" type="data" label="FASTA file" help="Select a FASTA file containing the sequences to be scanned."/> | |
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"/> | |
15 <param name="strand" type="select" label="Select sequence strands to scan" help="Scan either both strands or only the forward strand."> | |
16 <option value="0">Scan both strands</option> | |
17 <option value="1">Only scan forward strand</option> | |
18 </param> | |
19 </inputs> | |
20 <outputs> | |
21 <data format="gff" name="output" /> | |
22 </outputs> | |
23 <tests> | |
24 <test> | |
25 <param name="iupac" value="WGATAR" /> | |
26 <param name="fasta" value="phix.fa" /> | |
27 <param name="label" value="IUPAC_or_name" /> | |
28 <param name="strand" value="0" /> | |
29 <output name="output" file="iupac_each_match.gff" /> | |
30 </test> | |
31 </tests> | |
32 | |
33 <help> | |
34 .. class:: infomark | |
35 | |
36 **What it does** | |
37 | |
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. | |
39 | |
40 IUPAC = Nucleotide(s): | |
41 | |
42 A = A | |
43 | |
44 C = C | |
45 | |
46 G = G | |
47 | |
48 T = T | |
49 | |
50 M = A/C | |
51 | |
52 R = A/G | |
53 | |
54 W = A/T | |
55 | |
56 S = C/G | |
57 | |
58 Y = C/T | |
59 | |
60 K = G/T | |
61 | |
62 V = A/C/G | |
63 | |
64 H = A/C/T | |
65 | |
66 D = A/G/T | |
67 | |
68 B = C/G/T | |
69 | |
70 N = A/C/G/T | |
71 | |
72 ---- | |
73 | |
74 .. class:: infomark | |
75 | |
76 **Options** | |
77 | |
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. | |
79 | |
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. | |
81 | |
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). | |
83 | |
84 ---- | |
85 | |
86 .. class:: infomark | |
87 | |
88 **Credits** | |
89 | |
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. | |
91 | |
92 Please kindly acknowledge both this Galaxy tool and Scan_IUPAC_output_each_match.pl if you use it. | |
93 </help> | |
94 | |
95 </tool> | |
96 |