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comparison SMART/galaxy/WrappGetLetterDistribution.xml @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
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17:b0e8584489e6 18:94ab73e8a190
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</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
3 <command interpreter="python"> 6 <command interpreter="python">
4 WrappGetLetterDistribution.py -i $inputFileName 7 WrappGetLetterDistribution.py -i $inputFileName
5 #if $formatType.FormatInputFileName == 'fasta': 8 #if $formatType.FormatInputFileName == 'fasta':
6 -f fasta 9 -f fasta
7 #else : 10 #else :
23 </when> 26 </when>
24 </conditional> 27 </conditional>
25 </inputs> 28 </inputs>
26 29
27 <outputs> 30 <outputs>
28 <data name="ouputFileNameCSV" format="tabular" label="[getLetterDistribution] CSV File"/> 31 <data name="ouputFileNameCSV" format="tabular" label="[get letter distribution] CSV file"/>
29 <data name="ouputFileNamePNG1" format="png" label="[getLetterDistribution] PNG File 1"/> 32 <data name="ouputFileNamePNG1" format="png" label="[get letter distribution] PNG file 1"/>
30 <data name="ouputFileNamePNG2" format="png" label="[getLetterDistribution] PNG File 2"/> 33 <data name="ouputFileNamePNG2" format="png" label="[get letter distribution] PNG file 2"/>
31 </outputs> 34 </outputs>
32 <tests> 35 <tests>
33 <test> 36 <test>
34 <param name="FormatInputFileName" value="fastq" /> 37 <param name="FormatInputFileName" value="fastq" />
35 <param name="inputFileName" value="short_fastq.fastq" /> 38 <param name="inputFileName" value="short_fastq.fastq" />
36 <output name="outputFileNameCSV" file="exp_getletterdistribution_short_fastq.csv" /> 39 <output name="outputFileNameCSV" file="exp_getletterdistribution_short_fastq.csv" />
37 </test> 40 </test>
38 </tests> 41 </tests>
39 42
40 <help> 43 <help>
41 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**. 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**.
42 45
43 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. 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.
44 </help> 47 </help>
45 </tool> 48 </tool>