Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/WrappGetLetterDistribution.xml @ 27:4e7ee5683ef1
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:30:11 -0400 |
parents | 94ab73e8a190 |
children | 0ab839023fe4 |
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<tool id="getLetterDistribution1" name="get letter distribution"> <description>Calculate distribution for each nucleotide per position for all short reads</description> <requirements> <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> WrappGetLetterDistribution.py -i $inputFileName #if $formatType.FormatInputFileName == 'fasta': -f fasta #else : -f fastq #end if -c $ouputFileNameCSV -a $ouputFileNamePNG1 -b $ouputFileNamePNG2 </command> <inputs> <conditional name="formatType"> <param name="FormatInputFileName" type="select" label="Input File Format"> <option value="fasta">fasta</option> <option value="fastq" selected="true">fastq</option> </param> <when value="fasta"> <param name="inputFileName" format="fasta" type="data" label="Fasta Input File"/> </when> <when value="fastq"> <param name="inputFileName" format="fastq" type="data" label="Fastq Input File"/> </when> </conditional> </inputs> <outputs> <data name="ouputFileNameCSV" format="tabular" label="[get letter distribution] CSV file"/> <data name="ouputFileNamePNG1" format="png" label="[get letter distribution] PNG file 1"/> <data name="ouputFileNamePNG2" format="png" label="[get letter distribution] PNG file 2"/> </outputs> <tests> <test> <param name="FormatInputFileName" value="fastq" /> <param name="inputFileName" value="short_fastq.fastq" /> <output name="outputFileNameCSV" file="exp_getletterdistribution_short_fastq.csv" /> </test> </tests> <help> 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**. 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. </help> </tool>