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comparison SMART/galaxy/WrappGetLetterDistribution.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
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30:5677346472b5 31:0ab839023fe4
1 <tool id="getLetterDistribution1" name="get letter distribution"> 1 <tool id="getLetterDistribution1" name="Get Letter Distribution">
2 <description>Calculate distribution for each nucleotide per position for all short reads</description> 2 <description>Calculate distribution for each nucleotide per position for all short reads (S-MART)</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 WrappGetLetterDistribution.py -i $inputFileName 4 WrappGetLetterDistribution.py -i $inputFileName
8 #if $formatType.FormatInputFileName == 'fasta': 5 #if $formatType.FormatInputFileName == 'fasta':
9 -f fasta 6 -f fasta
10 #else : 7 #else :
26 </when> 23 </when>
27 </conditional> 24 </conditional>
28 </inputs> 25 </inputs>
29 26
30 <outputs> 27 <outputs>
31 <data name="ouputFileNameCSV" format="tabular" label="[get letter distribution] CSV file"/> 28 <data name="ouputFileNameCSV" format="tabular" label="[getLetterDistribution] CSV File"/>
32 <data name="ouputFileNamePNG1" format="png" label="[get letter distribution] PNG file 1"/> 29 <data name="ouputFileNamePNG1" format="png" label="[getLetterDistribution] PNG File 1"/>
33 <data name="ouputFileNamePNG2" format="png" label="[get letter distribution] PNG file 2"/> 30 <data name="ouputFileNamePNG2" format="png" label="[getLetterDistribution] PNG File 2"/>
34 </outputs> 31 </outputs>
35 <tests> 32 <tests>
36 <test> 33 <test>
37 <param name="FormatInputFileName" value="fastq" /> 34 <param name="FormatInputFileName" value="fastq" />
38 <param name="inputFileName" value="short_fastq.fastq" /> 35 <param name="inputFileName" value="short_fastq.fastq" />
39 <output name="outputFileNameCSV" file="exp_getletterdistribution_short_fastq.csv" /> 36 <output name="outputFileNameCSV" file="exp_getletterdistribution_short_fastq.csv" />
40 </test> 37 </test>
41 </tests> 38 </tests>
39 </tool>
42 40
43 <help>
44 The script gets the nucleotide distribution of the input sequence list. It outputs two files. The first file shows the nucleotide distribution of the data. More precisely, a point (*x*, *y*) on the curve **A** shows that *y* sequences have *x* % of **A**.
45
46 The second plot shows the average nucleotide distribution for each position of the read. You can use it to detect a bias in the first nucleotides, for instance. A point *x*, *y* on the curve **A** shows that at the position *x*, there are *y*% of **A**. A point (*x*, *y*) on the curve **#** tells you that *y* % of the sequences contain not less than *x* nucleotides. By definition, this latter line is a decreasing function. It usually explains why the tail of the other curves are sometimes erratic: there are few sequences.
47 </help>
48 </tool>