Mercurial > repos > xuebing > sharplabtool
view tools/metag_tools/short_reads_figure_high_quality_length.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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<tool id="hist_high_quality_score" name="Histogram"> <description> of high quality score reads </description> <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> <requirements> <requirement type="python-module">rpy</requirement> </requirements> <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>