Mercurial > repos > xuebing > sharplabtool

comparison tools/plotting/boxplot.xml @ 0:9071e359b9a3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
1 <tool id="qual_stats_boxplot" name="Boxplot" version="1.0.0">
2 <description>of quality statistics</description>
3 <command>gnuplot &lt; '$gnuplot_commands' 2&gt;&amp;1 || echo "Error running gnuplot." >&amp;2</command>
4 <requirements>
5 <requirement type="binary" version="gnuplot 4.2 patchlevel 2">gnuplot</requirement>
6 </requirements>
7 <inputs>
8 <param name="input_file" type="data" format="tabular" label="Quality Statistics File"/>
9 <param name="title" type="text" value="Box plot in Galaxy" label="Title for plot" size="50"/>
10 <param name="graph_size" type="text" value="2048,768" label="Dimensions of Graph"/>
11 <param name="xlabel" type="text" value="X Axis Label" label="X axis label" size="50"/>
12 <param name="ylabel" type="text" value="Score Value" label="Y axis label" size="50"/>
13 <param name="xcol" type="data_column" data_ref="input_file" label="Column for X axis position" default_value="1" help="A unique number; c1 if plotting output of FASTQ summary"/>
14 <param name="q1col" type="data_column" data_ref="input_file" label="Column for Q1" default_value="7" help="c7 if plotting output of FASTQ summary"/>
15 <param name="medcol" type="data_column" data_ref="input_file" label="Column for Median" default_value="8" help="c8 if plotting output of FASTQ summary"/>
16 <param name="q3col" type="data_column" data_ref="input_file" label="Column for Q3" default_value="9" help="c9 if plotting output of FASTQ summary"/>
17 <param name="lwcol" type="data_column" data_ref="input_file" label="Column for left whisker" default_value="11" help="c11 if plotting output of FASTQ summary"/>
18 <param name="rwcol" type="data_column" data_ref="input_file" label="Column for right whisker" default_value="12" help="c12 if plotting output of FASTQ summary"/>
19 <conditional name="use_outliers">
20 <param name="use_outliers_type" type="select" label="Plot Outliers">
21 <option value="use_outliers" selected="true">Plot Outliers</option>
22 <option value="dont_use_outliers">Don't Plot Outliers</option>
23 </param>
24 <when value="use_outliers">
25 <param name="outliercol" type="data_column" data_ref="input_file" label="Column for Outliers" default_value="13" help="c13 if plotting output of FASTQ summary"/>
26 </when>
27 <when value="dont_use_outliers">
28 </when>
29 </conditional>
30 </inputs>
31 <configfiles>
32 <configfile name="gnuplot_commands">
33 set output '$output_file'
34 set term png size ${graph_size}
35 set boxwidth 0.8
36 set key right tmargin
37 set xlabel "${xlabel}"
38 set ylabel "${ylabel}"
39 set title "${title}"
40 set xtics 1
41 set ytics 1
42 set grid ytics
43 set offsets 1, 1, 1, 1
44 plot '${input_file}' using ${xcol}:${q1col}:${lwcol}:${rwcol}:${q3col} with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, \
45 '' using ${xcol}:${medcol}:${medcol}:${medcol}:${medcol} with candlesticks lt -1 lw 2 title 'Medians'\
46 #if str( $use_outliers['use_outliers_type'] ) == 'use_outliers':
47 , "&lt; python -c \"for xval, yvals in [ ( fields[${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'
48 #end if
49 </configfile>
50 </configfiles>
51 <outputs>
52 <data name="output_file" format="png" />
53 </outputs>
54 <tests>
55 <test>
56 <param name="input_file" value="fastq_stats_1_out.tabular" ftype="tabular" />
57 <param name="title" value="Boxplot of Summary Statistics for Sanger Reads" />
58 <param name="graph_size" value="2048,768" />
59 <param name="xlabel" value="Read Column" />
60 <param name="ylabel" value="Quality Score Value" />
61 <param name="xcol" value="1" />
62 <param name="q1col" value="7" />
63 <param name="medcol" value="8" />
64 <param name="q3col" value="9" />
65 <param name="lwcol" value="11" />
66 <param name="rwcol" value="12" />
67 <param name="use_outliers_type" value="use_outliers" />
68 <param name="outliercol" value="13" />
69 <output name="output_file" file="boxplot_summary_statistics_out.png" />
70 </test>
71 </tests>
72 <help>
73
74 **What it does**
75
76 Creates a boxplot graph. Its main purpose is to display a distribution of quality scores produced by *NGS: QC and maniupulation -> FASTQ Summary Statistics* tool.
77
78 .. class:: warningmark
79
80 **TIP:** If you want to display a distribution of quality scores produced by *NGS: QC and maniupulation -> FASTQ Summary Statistics* and the column assignments within the tool's interface are not automatically set (they will all read "c1" in that case) set columns manually to the following values::
81
82 Column for X axis c1
83 Column for Q1 c7
84 Column for Median c8
85 Column for Q3 c9
86 Column for left whisker c11
87 Column for right whisker c12
88 Column for Outliers c13
89
90 -----
91
92 **Output Example**
93
94 * Black horizontal lines are medians
95 * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
96 * Whiskers show outliers at max. 1.5*IQR
97
98 .. image:: ./static/images/solid_qual.png
99
100
101 </help>
102 </tool>