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comparison compute_motifs_frequency.xml @ 0:46325357b948 draft

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author devteam
date Wed, 25 Sep 2013 10:05:37 -0400
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1 <tool id="compute_motifs_frequency" name="Compute Motif Frequencies" version="1.0.0">
2 <description>in indel flanking regions</description>
3
4
5 <command interpreter="perl">
6 compute_motifs_frequency.pl $inputFile1 $inputFile2 $inputNumber3 $outputFile1 $outputFile2
7 </command>
8
9
10 <inputs>
11
12 <param format="tabular" name="inputFile1" type="data" label="Select motifs file"/>
13
14 <param format="tabular" name="inputFile2" type="data" label="Select indel flanking regions file from your history"/>
15
16 <param type="integer" name="inputNumber3" size="5" value="0" label="What is the size of each window?" help="'0' = all the upstream flanking sequence will be one window only, and the same for the downstream flanking sequence."/>
17
18 </inputs>
19
20
21 <outputs>
22 <data format="tabular" name="outputFile1"/>
23 <data format="tabular" name="outputFile2"/>
24 </outputs>
25
26 <tests>
27 <test>
28 <param name="inputFile1" value="motifs1.tabular" />
29 <param name="inputFile2" value="indelsFlankingSequences1.tabular" />
30 <param name="inputNumber3" value="0" />
31 <output name="outputFile1" file="flankingSequencesWindows0.tabular" />
32 <output name="outputFile2" file="motifFrequencies0.tabular" />
33 </test>
34
35 <test>
36 <param name="inputFile1" value="motifs1.tabular" />
37 <param name="inputFile2" value="indelsFlankingSequences1.tabular" />
38 <param name="inputNumber3" value="10" />
39 <output name="outputFile1" file="flankingSequencesWindows10.tabular" />
40 <output name="outputFile2" file="motifFrequencies10.tabular" />
41 </test>
42 </tests>
43
44
45 <help>
46
47 .. class:: infomark
48
49 **What it does**
50
51 This program computes the frequency of motifs in the flanking regions of indels found in a chromosome or a genome.
52 Each indel has an upstream flanking sequence and a downstream flanking one. Each of the upstream and downstream flanking
53 sequences will be divided into a certain number of windows according to the window size input by the user.
54 The frequency of a motif in a certain window in one of the two flanking sequences is the total sum of occurrences of
55 that motif in that window of that flanking sequence over all indels. The indel flanking regions file will be taken
56 from your history or it will be uploaded, whereas the motifs file should be uploaded.
57
58 - The first input file is the motifs file and it is a tabular file consisting of two columns:
59
60 - the first column represents the motif name
61 - the second column represents the motif sequence, as follows::
62
63 dnaPolPauseFrameshift1 GAG
64 dnaPolPauseFrameshift2 ACG
65 xSites1 CCG
66
67 - The second input file is the indels flanking regions file and it is a tabular file consisting of five columns:
68
69 - the first column represents the indel start coordinate
70 - the second column represents the indel end coordinate
71 - the third column represents the indel length
72 - the fourth column represents the upstream flanking sequence
73 - the fifth column represents the upstream flanking sequence, as follows::
74
75 16694766 16694768 3 GTGGGTCCTGCCCAGCCTCTGCCTCAGAGGGAAGAGTAGAGAACTGGG AGAGCAGGTCCTTAGGGAGCCCGAGGAAGTCCCTGACGCCAGCTGTTCTCGCGGACGAA
76 25169542 25169545 4 caagcccacaagccttcagaccatagcaCGGGCTCCAGAGGTGTGAGG CAGGTCAGGTGCTTTAGAAGTCAAAAACTCTCAGTAAGGCAAATCACCCCCTATCTCCT
77 41929580 41929585 6 ggctgtcgtatggaatctggggctcaggactctgtcccatttctctaa accattctgcTTCAACCCAGACACTGACTGTTTTCCAAATTTACTTGTTTGTTTGTTTT
78
79
80 -----
81
82 .. class:: warningmark
83
84 **Notes**
85
86 - The lengths of the upstream flanking sequences must be equal for all indels.
87 - The lengths of the downstream flanking sequences must be equal for all indels.
88 - If the length of the upstream flanking sequence L is not an integer multiple of the window size S, in other words if L/S = m + r where m is the result of division and r is the remainder, then the upstream flanking sequence will be divided into m windows only starting from the indel, and the rest of the sequence will not be considered. The same rule applies to the downstream flanking sequence.
89
90 -----
91
92 The **output** of this program is two files:
93
94 - The first output file is a tabular file and represents the windows of both upstream and downstream flanking sequences. It consists of multiple left columns representing the windows of the upstream flanking sequence, followed by one column representing the indels, then followed by multiple right columns representing the windows of the downstream flanking sequence, as follows::
95
96 cgaggtcagg agatcgagac catcctggct aacatggtga aatcccgtct ctactaaaaa indel aaatttatat ttataaacaa ttttaataca cctatgttta ttatacattt
97 GCCAGTTTAT GGTCTAACAA GGAGAGAAAC AGGGGGCTGA AGGGGTTTCT TAACCTCCAG indel TTCCGGGCTC TGTCCCTAAC CCCCAGCTAG GTAAGTGGCA AAGCACTTCT
98 CAGTGGGACC AAGCACTGAA CCACTTTGGG GAGAATCTCA CACTGGGGCC CTCTGACACC indel tatatatttt tttttttttt tttttttttt tttttttttg agatggtgtc
99 AGAGCAGCAG CACCCACTTT TGCAGTGTGT GACGTTGGTG GAGCCATCGA AGTCTGTGCT indel GAGCCCTCCC CAGTGCTCCG AGGAGCTGCT GTTCCCCCTG GAGCTCAGAA
100
101 - The second output file is a tabular file and represents the motif frequencies in every window of every flanking sequence. The first column on the left represents the names of motifs. The other columns represent the frequencies of motifs in the windows that correspond to the ones in the first output file, as follows::
102
103 dnaPolPauseFrameshift1 2 3 1 0 1 2 indel 0 2 2 1 3
104 dnaPolPauseFrameshift2 2 3 1 0 1 2 indel 0 2 2 1 3
105 xSites1 3 2 0 1 1 2 indel 1 1 3 2 3
106
107 </help>
108
109 </tool>