/tools/metag_tools/short_reads_figure_score.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 87 lines · 62 code · 25 blank · 0 comment · 0 complexity · f0a0865e7d092d148e5acd40218ce045 MD5 · raw file
- <tool id="quality_score_distribution" name="Build base quality distribution" version="1.0.2">
- <description></description>
- <command interpreter="python">short_reads_figure_score.py $input1 $output1 </command>
- <inputs>
- <page>
- <param name="input1" type="data" format="qualsolexa, qual454" label="Quality score file" help="No dataset? Read tip below"/>
- </page>
- </inputs>
- <outputs>
- <data name="output1" format="png" />
- </outputs>
- <requirements>
- <requirement type="python-module">rpy</requirement>
- </requirements>
- <tests>
- <test>
- <param name="input1" value="solexa.qual" ftype="qualsolexa" />
- <output name="output1" file="solexaScore.png" ftype="png" />
- </test>
- <test>
- <param name="input1" value="454.qual" ftype="qual454" />
- <output name="output1" file="454Score.png" ftype="png" />
- </test>
- </tests>
- <help>
- .. class:: warningmark
- To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples).
- -----
- **What it does**
- This tool takes Quality Files generated by Roche (454), Illumina (Solexa), or ABI SOLiD machines and builds a graph showing score distribution like the one below. Such graph allows you to perform initial evaluation of data quality in a single pass.
- -----
- **Examples of Quality Data**
- Roche (454) or ABI SOLiD data::
- >seq1
- 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28
- Illumina (Solexa) data::
- -40 -40 40 -40 -40 -40 -40 40
-
- -----
- **Output example**
- Quality scores are summarized as boxplot (Roche 454 FLX data):
- .. image:: ${static_path}/images/short_reads_boxplot.png
- where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines:
- - For Roche (454) X-axis (shown above) indicates **relative** position (in %) within reads as this technology produces reads of different lengths;
- - For Illumina (Solexa) and ABI SOLiD X-axis shows **absolute** position in nucleotides within reads.
-
- Every box on the plot shows the following values::
- o <---- Outliers
- o
- -+- <---- Upper Extreme Value that is no more
- | than box length away from the box
- |
- +--+--+ <---- Upper Quartile
- | |
- +-----+ <---- Median
- | |
- +--+--+ <---- Lower Quartile
- |
- |
- -+- <---- Lower Extreme Value that is no more
- than box length away from the box
- o <---- Outlier
-
-
-
- </help>
- </tool>