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Add a new FASTQ tool suite. Four FASTQ variants are supported: sanger, illumina, solexa and solid.

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Tools include:
	FASTQ Groomer convert between various FASTQ quality formats
	Combine FASTA and QUAL into FASTQ
	FASTQ joiner on paired end reads
	FASTQ splitter on joined paired end reads
	FASTQ to FASTA converter
	FASTQ Summary Statistics by column
	Filter FASTQ reads by quality score and length
	FASTQ Trimmer by column
	Manipulate FASTQ reads on various attributes
	Boxplot of quality statistics (Generic, with outliers)
This commit is contained in:
Daniel Blankenberg
2010-02-23 16:48:07 -05:00
parent ea7f5879e1
commit 8082c6f36f
31 changed files with 2721 additions and 9 deletions
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tools/plotting/boxplot.xml
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<tool id="qual_stats_boxplot" name="Boxplot" version="1.0.0">
<description>of quality statistics</description>
<command>gnuplot &lt; '$gnuplot_commands' &gt; '$output_file'</command>
<inputs>
<param name="input_file" type="data" format="tabular" label="Quality Statistics File"/>
<param name="title" type="text" value="Box plot in Galaxy" label="Title for plot" size="50"/>
<param name="graph_size" type="text" value="2048,768" label="Dimensions of Graph"/>
<param name="xlabel" type="text" value="X Axis Label" label="X axis label" size="50"/>
<param name="ylabel" type="text" value="Score Value" label="Y axis label" size="50"/>
<param name="xcol" type="data_column" data_ref="input_file" label="Column for X axis position" default_value="1" help="A unique number"/>
<param name="q1col" type="data_column" data_ref="input_file" label="Column for Q1" default_value="7"/>
<param name="medcol" type="data_column" data_ref="input_file" label="Column for Median" default_value="8"/>
<param name="q3col" type="data_column" data_ref="input_file" label="Column for Q3" default_value="9"/>
<param name="lwcol" type="data_column" data_ref="input_file" label="Column for left whisker" default_value="11"/>
<param name="rwcol" type="data_column" data_ref="input_file" label="Column for right whisker" default_value="12"/>
<conditional name="use_outliers">
<param name="use_outliers_type" type="select" label="Plot Outliers">
<option value="use_outliers" selected="true">Plot Outliers</option>
<option value="dont_use_outliers">Don't Plot Outliers</option>
</param>
<when value="use_outliers">
<param name="outliercol" type="data_column" data_ref="input_file" label="Column for Outliers" default_value="13"/>
</when>
<when value="dont_use_outliers">
</when>
</conditional>
</inputs>
<configfiles>
<configfile name="gnuplot_commands">
set term png size ${graph_size}
set boxwidth 0.8
set key right tmargin
set xlabel "${xlabel}"
set ylabel "${ylabel}"
set title "${title}"
set xtics 1
set ytics 1
set grid ytics
set offsets 1, 1, 1, 1
plot '${input_file}' using ${xcol}:${q1col}:${lwcol}:${rwcol}:${q3col} with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, \
'' using ${xcol}:${medcol}:${medcol}:${medcol}:${medcol} with candlesticks lt -1 lw 2 title 'Medians'\
#if str( $use_outliers['use_outliers_type'] ) == 'use_outliers':
, "&lt; python -c \"for xval, yvals in [ ( fields[${xcol} - 1], fields[${use_outliers['outliercol']} - 1].split( ',' ) ) for fields in [ line.rstrip( '\\n\\r' ).split( '\\t' ) for line in open( '${input_file}' ) if not line.startswith( '#' ) ] if len( fields ) &gt; max( ${xcol} - 1, ${use_outliers['outliercol']} - 1 ) ]: print '\\n'.join( [ '%s\\t%s' % ( xval, yval ) for yval in yvals if yval ] )\"" using 1:2 with points pt 29 title 'Outliers'
#end if
</configfile>
</configfiles>
<outputs>
<data name="output_file" format="png" />
</outputs>
<tests>
<test>
<param name="input_file" value="fastq_stats_1_out.tabular" ftype="tabular" />
<param name="title" value="Boxplot of Summary Statistics for Sanger Reads" />
<param name="graph_size" value="2048,768" />
<param name="xlabel" value="Read Column" />
<param name="ylabel" value="Quality Score Value" />
<param name="xcol" value="1" />
<param name="q1col" value="7" />
<param name="medcol" value="8" />
<param name="q3col" value="9" />
<param name="lwcol" value="11" />
<param name="rwcol" value="12" />
<param name="use_outliers_type" value="use_outliers" />
<param name="outliercol" value="13" />
<output name="output_file" file="boxplot_summary_statistics_out.png" />
</test>
</tests>
<help>
This tool creates a boxplot from a tabular file containing summary statistics.
Outliers are optionally defined using a comma-separated list of values.
</help>
</tool>