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comparison pyCRAC/pySelectMotifsFromGTF.xml @ 0:19b20927172d draft

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author swebb
date Tue, 18 Jun 2013 09:11:00 -0400
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1 <tool id ="pySelectMotifsFromGTF" name="pySelectMotifsFromGTF">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="python">
6 /usr/local/bin/pySelectMotifsFromGTF.py
7 --gtf $input
8 -m $motif
9 -o $out
10 -l $length
11 -z $zscore
12 </command>
13 <version_command>/usr/local/bin/pySelectMotifsFromGTF.py --version</version_command>
14 <inputs>
15 <param format="gtf" name="input" type="data" label="Input File -f" help="pyMotif gtf output files" />
16 <param format="txt" name="motif" type="text" size="200" value="KBCTTG" label="motif string" help="Enter motif (all uppercase) you want to extract from the pyMotif gtf output file">
17 <validator type="empty_field" />
18 </param>
19 <param format="integer" type="integer" value="6" size="5" name="length" label="Length --length" help="Set a Kmer Length. Note that the length has to be at least as long as your k-mer sequence, otherwise the program will not run correctly" />
20 <param format="float" type="float" value="0" size="5" name="zscore" label="Z Score --Z_score" help="Set a minimum Kmer Z_score" />
21 <param name="label" type="text" format="txt" size="30" value="pySelectMotifsFromGTF" label="Enter output file label -o" />
22 </inputs>
23
24 <outputs>
25 <data format="gtf" name="out" label="${label.value}_${motif.value}.gtf"/>
26 </outputs>
27 <help>
28
29
30 .. class:: infomark
31
32 **pySelectMotifsFromGTF**
33
34 pySelectMotifsFromGTF is part of the pyCRAC_ package. Extracts your favourite k-mer sequence from pyMotif GTF output files.
35 Note that you can include degenerate nucleotides in your motif string::
36
37 N = A, G, C or T
38 R = A or G = puRine
39 Y = C or T = pYrimidine
40 M = A or C = aroMatic
41 S = G or C
42 W = A or T
43 K = G or T = Keto
44 V = A, C or G = Not T (letter after)
45 D = A, G or T = Not C
46 H = A, C or T = Not G
47 B = C, G or T = Not A
48
49 So if you enter KBCTTG as search string and length=6, then the program will extract a large number of six-mers from your data.
50 If you set length = 8, it will look for this pattern in a stretch of 8 nucleotides.
51
52 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
53
54 ------
55
56 **Parameter list**
57
58 Options::
59
60 --gtf=Yourfavoritegtf.gtf
61 type the path to the gtf file that you want to use. By
62 default it expects data from the standard input
63 -o FILE, --output=FILE
64 Optional.Specify the name of the output file. Default
65 is standard output. Make sure it has the .gtf
66 extension!
67 -m KBCTTG, --motif=KBCTTG
68 Specify the motif you want extract from the GTF file.
69 -z 15.0, --Z_score=15.0
70 Set a minimum k-mer Z-score. Default=0
71 -l 4, --length=4
72 Set a k-mer length. Default is no length filtering
73
74 </help>
75 </tool>