Mercurial > repos > devteam > scatterplot
changeset 3:efda9a4a50e7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit 405b0656c97b3971605e09f77cf46ca1f4870346
| author | devteam |
|---|---|
| date | Sat, 03 Jun 2017 09:29:30 -0400 |
| parents | 4f8b9e70fda0 |
| children | |
| files | scatterplot.py scatterplot.xml |
| diffstat | 2 files changed, 23 insertions(+), 10 deletions(-) [+] |
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--- a/scatterplot.py Thu Sep 15 11:14:37 2016 -0400 +++ b/scatterplot.py Sat Jun 03 09:29:30 2017 -0400 @@ -1,6 +1,8 @@ #!/usr/bin/env python # Greg Von Kuster +from __future__ import print_function + import sys from numpy import array @@ -35,7 +37,7 @@ invalid_value = '' invalid_column = 0 i = 0 - for i, line in enumerate( file( in_fname ) ): + for i, line in enumerate( open( in_fname ) ): valid = True line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ): @@ -74,14 +76,14 @@ r.pdf( out_fname, 8, 8 ) r.plot( a, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 ) r.dev_off() - except Exception, exc: + except Exception as exc: stop_err( "%s" % str( exc ) ) else: stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) ) - print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] ) + print("Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] )) if skipped_lines > 0: - print "Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column ) + print("Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column )) if __name__ == "__main__": main()
--- a/scatterplot.xml Thu Sep 15 11:14:37 2016 -0400 +++ b/scatterplot.xml Sat Jun 03 09:29:30 2017 -0400 @@ -1,12 +1,20 @@ -<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.2"> +<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.3"> <description>of two numeric columns</description> <requirements> <requirement type="package" version="1.9">numpy</requirement> - <!-- explicit R requirement is necessary for toolshed package, conda rpy2 comes with R --> - <requirement type="package" version="3.2.1">R</requirement> - <requirement type="package" version="2.7.8">rpy2</requirement> + <requirement type="package" version="2.8.5">rpy2</requirement> </requirements> - <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command> + <command><![CDATA[ + python '$__tool_directory__/scatterplot.py' + '$input' + '$out_file1' + $col1 + $col2 + '$title' + '$xlab' + '$ylab' + ]]> + </command> <inputs> <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/> <param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" /> @@ -29,7 +37,7 @@ <output name="out_file1" file="scatterplot_out1.pdf" compare="sim_size" /> </test> </tests> - <help> + <help><![CDATA[ .. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* @@ -65,5 +73,8 @@ - Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset. .. image:: scatterplot.png +]]> </help> +<citations> +</citations> </tool>