Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/WrappGetLetterDistribution.xml @ 38:2c0c0a89fad7
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| author | m-zytnicki |
|---|---|
| date | Thu, 02 May 2013 09:56:47 -0400 |
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| 37:d22fadc825e3 | 38:2c0c0a89fad7 |
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| 1 <tool id="getLetterDistribution1" name="get letter distribution"> | |
| 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> | |
| 6 <command interpreter="python"> | |
| 7 WrappGetLetterDistribution.py -i $inputFileName | |
| 8 #if $formatType.FormatInputFileName == 'fasta': | |
| 9 -f fasta | |
| 10 #else : | |
| 11 -f fastq | |
| 12 #end if | |
| 13 -c $ouputFileNameCSV -a $ouputFileNamePNG1 -b $ouputFileNamePNG2 | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <conditional name="formatType"> | |
| 17 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 18 <option value="fasta">fasta</option> | |
| 19 <option value="fastq" selected="true">fastq</option> | |
| 20 </param> | |
| 21 <when value="fasta"> | |
| 22 <param name="inputFileName" format="fasta" type="data" label="Fasta Input File"/> | |
| 23 </when> | |
| 24 <when value="fastq"> | |
| 25 <param name="inputFileName" format="fastq" type="data" label="Fastq Input File"/> | |
| 26 </when> | |
| 27 </conditional> | |
| 28 </inputs> | |
| 29 | |
| 30 <outputs> | |
| 31 <data name="ouputFileNameCSV" format="tabular" label="[get letter distribution] CSV file"/> | |
| 32 <data name="ouputFileNamePNG1" format="png" label="[get letter distribution] PNG file 1"/> | |
| 33 <data name="ouputFileNamePNG2" format="png" label="[get letter distribution] PNG file 2"/> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="FormatInputFileName" value="fastq" /> | |
| 38 <param name="inputFileName" value="short_fastq.fastq" /> | |
| 39 <output name="outputFileNameCSV" file="exp_getletterdistribution_short_fastq.csv" /> | |
| 40 </test> | |
| 41 </tests> | |
| 42 | |
| 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> |