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Modified help section and help tags to ease paremeter selection by the user

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Anton Nekrutenko
2010-12-03 09:57:45 -05:00
parent 7b7453366f
commit 2763d08d86
1 changed files with 35 additions and 9 deletions
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tools/plotting/boxplot.xml
+35 -9
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@@ -10,19 +10,19 @@
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
</when>
<when value="dont_use_outliers">
</when>
@@ -70,7 +70,33 @@ plot '${input_file}' using ${xcol}:${q1col}:${lwcol}:${rwcol}:${q3col} with cand
</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.
**What it does**
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.
.. class:: warningmark
**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::
Column for X axis c1
Column for Q1 c7
Column for Median c8
Column for Q3 c9
Column for left whisker c11
Column for right whisker c12
Column for Outliers c13
-----
**Output Example**
* Black horizontal lines are medians
* Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
* Whiskers show outliers at max. 1.5*IQR
.. image:: ../static/images/solid_qual.png
</help>
</tool>