Mercurial > repos > devteam > short_reads_figure_high_quality_length
diff short_reads_figure_high_quality_length.xml @ 0:556ceed24699 draft
Imported from capsule None
author | devteam |
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date | Mon, 19 May 2014 12:34:37 -0400 |
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children | 76c4a4ed8e74 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/short_reads_figure_high_quality_length.xml Mon May 19 12:34:37 2014 -0400 @@ -0,0 +1,74 @@ +<tool id="hist_high_quality_score" name="Histogram" version="1.0.0"> +<description> of high quality score reads </description> +<requirements> + <requirement type="package" version="1.0.3">rpy</requirement> + <requirement type="package" version="2.11.0">R</requirement> +</requirements> +<command interpreter="python">short_reads_figure_high_quality_length.py $input1 $output1 $input2</command> +<inputs> +<page> + <param name="input1" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/> + <param name="input2" type="integer" size="5" value="20" label="Quality score threshold" /> +</page> +</inputs> +<outputs> + <data name="output1" format="pdf" /> +</outputs> +<tests> + <test> + <param name="input1" value="solexa.qual" ftype="qualsolexa" /> + <param name="input2" value="5" /> + <output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/> + </test> + <test> + <param name="input1" value="454.qual" ftype="qual454" /> + <param name="input2" value="5" /> + <output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/> + </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 histogram of lengths of high quality reads. + +----- + +**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 + +----- + +**Note** + +- Quality score data:: + + >seq1 + 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 + +- If the threshold is set to 20: + + - a low quality score 4 in the middle separated two segments of lengths 11 and 5. + + - The histogram will be built based on the numbers (11, 5). + +- For Illumina (Solexa) data, only the maximal of the 4 values will be used. + + +</help> +</tool>