Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/WrappGetLetterDistribution.xml @ 36:44d5973c188c
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 15:02:29 -0400 |
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| 35:d94018ca4ada | 36:44d5973c188c |
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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 <command interpreter="python"> | |
| 4 WrappGetLetterDistribution.py -i $inputFileName | |
| 5 #if $formatType.FormatInputFileName == 'fasta': | |
| 6 -f fasta | |
| 7 #else : | |
| 8 -f fastq | |
| 9 #end if | |
| 10 -c $ouputFileNameCSV -a $ouputFileNamePNG1 -b $ouputFileNamePNG2 | |
| 11 </command> | |
| 12 <inputs> | |
| 13 <conditional name="formatType"> | |
| 14 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 15 <option value="fasta">fasta</option> | |
| 16 <option value="fastq" selected="true">fastq</option> | |
| 17 </param> | |
| 18 <when value="fasta"> | |
| 19 <param name="inputFileName" format="fasta" type="data" label="Fasta Input File"/> | |
| 20 </when> | |
| 21 <when value="fastq"> | |
| 22 <param name="inputFileName" format="fastq" type="data" label="Fastq Input File"/> | |
| 23 </when> | |
| 24 </conditional> | |
| 25 </inputs> | |
| 26 | |
| 27 <outputs> | |
| 28 <data name="ouputFileNameCSV" format="tabular" label="[getLetterDistribution] CSV File"/> | |
| 29 <data name="ouputFileNamePNG1" format="png" label="[getLetterDistribution] PNG File 1"/> | |
| 30 <data name="ouputFileNamePNG2" format="png" label="[getLetterDistribution] PNG File 2"/> | |
| 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> | |
| 45 </tool> |