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77 lines
4.1 KiB
XML
77 lines
4.1 KiB
XML
<tool id="qual_stats_boxplot" name="Boxplot" version="1.0.0">
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<description>of quality statistics</description>
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<command>gnuplot < '$gnuplot_commands' 2>&1 || echo "Error running gnuplot." >&2</command>
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<requirements>
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<requirement type="binary" version="gnuplot 4.2 patchlevel 2">gnuplot</requirement>
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</requirements>
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<inputs>
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<param name="input_file" type="data" format="tabular" label="Quality Statistics File"/>
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<param name="title" type="text" value="Box plot in Galaxy" label="Title for plot" size="50"/>
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<param name="graph_size" type="text" value="2048,768" label="Dimensions of Graph"/>
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<param name="xlabel" type="text" value="X Axis Label" label="X axis label" size="50"/>
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<param name="ylabel" type="text" value="Score Value" label="Y axis label" size="50"/>
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<param name="xcol" type="data_column" data_ref="input_file" label="Column for X axis position" default_value="1" help="A unique number"/>
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<param name="q1col" type="data_column" data_ref="input_file" label="Column for Q1" default_value="7"/>
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<param name="medcol" type="data_column" data_ref="input_file" label="Column for Median" default_value="8"/>
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<param name="q3col" type="data_column" data_ref="input_file" label="Column for Q3" default_value="9"/>
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<param name="lwcol" type="data_column" data_ref="input_file" label="Column for left whisker" default_value="11"/>
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<param name="rwcol" type="data_column" data_ref="input_file" label="Column for right whisker" default_value="12"/>
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<conditional name="use_outliers">
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<param name="use_outliers_type" type="select" label="Plot Outliers">
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<option value="use_outliers" selected="true">Plot Outliers</option>
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<option value="dont_use_outliers">Don't Plot Outliers</option>
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</param>
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<when value="use_outliers">
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<param name="outliercol" type="data_column" data_ref="input_file" label="Column for Outliers" default_value="13"/>
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</when>
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<when value="dont_use_outliers">
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</when>
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</conditional>
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</inputs>
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<configfiles>
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<configfile name="gnuplot_commands">
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set output '$output_file'
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set term png size ${graph_size}
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set boxwidth 0.8
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set key right tmargin
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set xlabel "${xlabel}"
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set ylabel "${ylabel}"
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set title "${title}"
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set xtics 1
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set ytics 1
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set grid ytics
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set offsets 1, 1, 1, 1
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plot '${input_file}' using ${xcol}:${q1col}:${lwcol}:${rwcol}:${q3col} with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, \
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'' using ${xcol}:${medcol}:${medcol}:${medcol}:${medcol} with candlesticks lt -1 lw 2 title 'Medians'\
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#if str( $use_outliers['use_outliers_type'] ) == 'use_outliers':
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, "< python -c \"for xval, yvals in [ ( fields[${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 ) > 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'
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#end if
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</configfile>
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</configfiles>
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<outputs>
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<data name="output_file" format="png" />
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</outputs>
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<tests>
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<test>
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<param name="input_file" value="fastq_stats_1_out.tabular" ftype="tabular" />
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<param name="title" value="Boxplot of Summary Statistics for Sanger Reads" />
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<param name="graph_size" value="2048,768" />
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<param name="xlabel" value="Read Column" />
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<param name="ylabel" value="Quality Score Value" />
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<param name="xcol" value="1" />
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<param name="q1col" value="7" />
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<param name="medcol" value="8" />
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<param name="q3col" value="9" />
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<param name="lwcol" value="11" />
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<param name="rwcol" value="12" />
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<param name="use_outliers_type" value="use_outliers" />
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<param name="outliercol" value="13" />
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<output name="output_file" file="boxplot_summary_statistics_out.png" />
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</test>
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</tests>
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<help>
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This tool creates a boxplot from a tabular file containing summary statistics.
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Outliers are optionally defined using a comma-separated list of values.
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</help>
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</tool>
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