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comparison SMART/galaxy/WrappGetLetterDistribution.xml @ 15:440ceca58672

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author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
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14:c79b9ae3f65f 15:440ceca58672
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 (S-MART)</description> 2 <description>Calculate distribution for each nucleotide per position for all short reads</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 WrappGetLetterDistribution.py -i $inputFileName 4 WrappGetLetterDistribution.py -i $inputFileName
5 #if $formatType.FormatInputFileName == 'fasta': 5 #if $formatType.FormatInputFileName == 'fasta':
6 -f fasta 6 -f fasta
7 #else : 7 #else :
26 26
27 <outputs> 27 <outputs>
28 <data name="ouputFileNameCSV" format="tabular" label="[getLetterDistribution] CSV File"/> 28 <data name="ouputFileNameCSV" format="tabular" label="[getLetterDistribution] CSV File"/>
29 <data name="ouputFileNamePNG1" format="png" label="[getLetterDistribution] PNG File 1"/> 29 <data name="ouputFileNamePNG1" format="png" label="[getLetterDistribution] PNG File 1"/>
30 <data name="ouputFileNamePNG2" format="png" label="[getLetterDistribution] PNG File 2"/> 30 <data name="ouputFileNamePNG2" format="png" label="[getLetterDistribution] PNG File 2"/>
31 </outputs> 31 </outputs>
32 <tests>
33 <test>
34 <param name="FormatInputFileName" value="fastq" />
35 <param name="inputFileName" value="short_fastq.fastq" />
36 <output name="outputFileNameCSV" file="exp_getletterdistribution_short_fastq.csv" />
37 </test>
38 </tests>
39
40 <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**.
42
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.
44 </help>
32 </tool> 45 </tool>
33