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https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Fixed scatterplot tool to use ColumnList parameter and deleted some unused files.
This commit is contained in:
Greg Von Kuster
@@ -62,6 +62,7 @@ def main():
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r.hist( a, probability=True, main=title, xlab=xlab, breaks=breaks )
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if density:
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r.lines( r.density( a ) )
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r.dev_off()
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except exc:
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stop_err("Building histogram resulted in error: %s." %str( exc ))
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else:
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@@ -70,5 +71,7 @@ def main():
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if skipped_lines > 0:
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print "..skipped %d invalid lines starting with line #%d. Value '%s' is not numeric." % ( skipped_lines, first_invalid_line, invalid_value )
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r.quit( save="no" )
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if __name__ == "__main__":
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main()
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@@ -1,31 +0,0 @@
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<tool id="Histogram1" name="Histogram">
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<description>for any numeric column</description>
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<command interpreter="python">plotter.py $input $col $bins $out_file1 hist</command>
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<inputs>
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<!-- <display>on column $col of $input with $bins bins</display> -->
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<param format="text" name="input" type="data" label="Select Query" />
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<param name="col" size="4" type="integer" value="5" label="Column to plot" />
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<param name="bins" size="4" type="integer" value="10" label="Number of bins" />
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</inputs>
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<outputs>
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<data format="png" name="out_file1" />
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</outputs>
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<code file="plot_filter.py"/>
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<help>
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This tool builds a simple histogram for a given data column using a specified number of bins:
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-----
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**Syntax**
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- **Column to plot** is an integer. The first column is **1**
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- **Number of bins** is an integer between 1 and 99
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-----
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**Example**
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.. image:: ../static/images/histogram.png
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</help>
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</tool>
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@@ -1,32 +0,0 @@
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<tool id="Scatterplot1" name="Scatterplot">
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<description>for any numeric column</description>
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<command interpreter="python">plotter.py $input $col $style $out_file1 scatter</command>
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<inputs>
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<!-- <display>on column $col of $input show $style</display> -->
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<param format="text" name="input" type="data" label="Select Query"/>
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<param name="col" size="4" type="integer" value="5" label="Column to plot"/>
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<param name="style" type="select" label="Plot style">
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<option value="L">Lines</option>
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<option value="P">Points</option>
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<option value="LP">Lines&Points</option>
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</param>
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</inputs>
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<outputs>
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<data format="png" name="out_file1" />
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</outputs>
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<help>This tool creates a simple scatterplot for a selected Query
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-----
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**Syntax**
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- **Column to plot** is an integer. The first column is **1**
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-----
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**Example**
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.. image:: ../static/images/scatter.png
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</help>
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</tool>
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@@ -2,16 +2,12 @@
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<description>of two numeric columns</description>
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<command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command>
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<inputs>
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<page>
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<param name="input" format="tabular" type="data" label="Dataset" help="Query missing? See TIP below"/>
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</page>
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<page>
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<param name="col1" type="select" label="Column for x axis" dynamic_options="get_columns( input )" />
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<param name="col2" type="select" label="Column for y axis" dynamic_options="get_columns( input )" />
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<param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/>
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<param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>
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<param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/>
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</page>
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<param name="input" type="data" format="tabular" label="Dataset" refresh_on_change="True" help="Query missing? See TIP below"/>
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<param name="col1" type="columnlist" assoc_dataset="input" numerical="True" label="Numerical column for x axis" />
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<param name="col2" type="columnlist" assoc_dataset="input" numerical="True" label="Numerical column for y axis" />
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<param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/>
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<param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>
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<param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/>
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</inputs>
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<outputs>
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<data format="pdf" name="out_file1" />
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@@ -55,5 +51,4 @@ This tool creates a simple scatter plot between two variables containing numeric
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.. image:: ../static/images/scatterplot.png
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</help>
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<code file="scatterplot_code.py" />
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</tool>
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@@ -1,42 +0,0 @@
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def get_columns( input ):
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columns = []
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elems = []
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for i, line in enumerate( file ( input.file_name ) ):
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valid = True
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if line and not line.startswith( '#' ):
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line = line.rstrip('\r\n')
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elems = line.split( '\t' )
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"""
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Since this tool requires users to select only those columns
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that contain numerical values, we'll restrict the column select
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list appropriately.
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"""
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if len(elems) > 0:
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for col in range(1, input.metadata.columns+1):
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try:
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val = float(elems[col-1])
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valid = True
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except:
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val = elems[col-1]
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if val:
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if val.strip().lower() == "na":
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valid = True
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else:
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valid = False
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else:
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valid = False
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if valid:
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option = "c" + str(col)
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columns.append((option,str(col),False))
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if len(columns) > 0:
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"""
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We have our select list built, so we can break out of the outer most for loop
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"""
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break
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if i == 30:
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break # Hopefully we never get here...
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return columns
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