Mercurial > repos > devteam > xy_plot
diff xy_plot.xml @ 3:319fa5a9fc1b draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
| author | devteam |
|---|---|
| date | Wed, 07 Dec 2016 18:29:23 -0500 |
| parents | 23657fcaaa5c |
| children | ecb437f1d298 |
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--- a/xy_plot.xml Fri Oct 09 15:50:24 2015 -0400 +++ b/xy_plot.xml Wed Dec 07 18:29:23 2016 -0500 @@ -1,151 +1,187 @@ -<tool id="XY_Plot_1" name="Plotting tool" version="1.0.1"> - <description>for multiple series and graph types</description> - <requirements> - <requirement type="package" version="2.11.0">R</requirement> - </requirements> - <command interpreter="bash">r_wrapper.sh $script_file</command> - - <inputs> - <param name="main" type="text" value="" label="Plot Title"/> - <param name="xlab" type="text" value="" label="Label for x axis"/> - <param name="ylab" type="text" value="" label="Label for y axis"/> - <repeat name="series" title="Series"> - <param name="input" type="data" format="tabular" label="Dataset"/> - <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/> - <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/> - <conditional name="series_type"> - <param name="type" type="select" label="Series Type"> - <option value="line" selected="true">Line</option> - <option value="points">Points</option> - </param> - <when value="line"> - <param name="lty" type="select" label="Line Type"> - <option value="1">Solid</option> - <option value="2">Dashed</option> - <option value="3">Dotted</option> - </param> - <param name="col" type="select" label="Line Color"> - <option value="1">Black</option> - <option value="2">Red</option> - <option value="3">Green</option> - <option value="4">Blue</option> - <option value="5">Cyan</option> - <option value="6">Magenta</option> - <option value="7">Yellow</option> - <option value="8">Gray</option> - </param> - <param name="lwd" type="float" label="Line Width" value="1.0"/> - </when> - <when value="points"> - <param name="pch" type="select" label="Point Type"> - <option value="1">Circle (hollow)</option> - <option value="2">Triangle (hollow)</option> - <option value="3">Cross</option> - <option value="4">Diamond (hollow)</option> - <option value="15">Square (filled)</option> - <option value="16">Circle (filled)</option> - <option value="17">Triangle (filled)</option> - </param> - <param name="col" type="select" label="Point Color"> - <option value="1">Black</option> - <option value="2">Red</option> - <option value="3">Green</option> - <option value="4">Blue</option> - <option value="5">Cyan</option> - <option value="6">Magenta</option> - <option value="7">Yellow</option> - <option value="8">Gray</option> - </param> - <param name="cex" type="float" label="Point Scale" value="1.0"/> - </when> - </conditional> - </repeat> - </inputs> - - <configfiles> - <configfile name="script_file"> - ## Setup R error handling to go to stderr - options( show.error.messages=F, - error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) - ## Determine range of all series in the plot - xrange = c( NULL, NULL ) - yrange = c( NULL, NULL ) - #for $i, $s in enumerate( $series ) - s${i} = read.table( "${s.input.file_name}" ) - x${i} = s${i}[,${s.xcol}] - y${i} = s${i}[,${s.ycol}] - xrange = range( x${i}, xrange ) - yrange = range( y${i}, yrange ) - #end for - ## Open output PDF file - pdf( "${out_file1}" ) - ## Dummy plot for axis / labels - plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" ) - ## Plot each series - #for $i, $s in enumerate( $series ) - #if $s.series_type['type'] == "line" - lines( x${i}, y${i}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} ) - #elif $s.series_type.type == "points" - points( x${i}, y${i}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} ) - #end if - #end for - ## Close the PDF file - devname = dev.off() - </configfile> - </configfiles> - - <outputs> - <data format="pdf" name="out_file1" /> - </outputs> - - <tests> - <test> - <param name="main" value="Example XY Plot"/> - <param name="xlab" value="Column 1"/> - <param name="ylab" value="Column 2"/> - <param name="input" value="2.tabular" ftype="tabular"/> - <param name="xcol" value="1"/> - <param name="ycol" value="2"/> - <param name="type" value="line"/> - <param name="lty" value="2"/> - <param name="col" value="2"/> - <param name="lwd" value="1.0"/> - <output name="out_file1" file="XY_Plot_1_out.pdf"/> - </test> - </tests> -<help> -.. class:: infomark - -This tool allows you to plot values contained in columns of a dataset against each other and also allows you to have different series corresponding to the same or different datasets in one plot. - ------ - -.. class:: warningmark - -This tool throws an error if the columns selected for plotting are absent or are not numeric and also if the lengths of these columns differ. - ------ - -**Example** - -Input file:: - - 1 68 4.1 - 2 71 4.6 - 3 62 3.8 - 4 75 4.4 - 5 58 3.2 - 6 60 3.1 - 7 67 3.8 - 8 68 4.1 - 9 71 4.3 - 10 69 3.7 - -Create a two series XY plot on the above data: - -- Series 1: Red Dashed-Line plot between columns 1 and 2 -- Series 2: Blue Circular-Point plot between columns 3 and 2 - -.. image:: xy_example.jpg -</help> -</tool> +<tool id="XY_Plot_1" name="Plotting tool" version="1.0.2"> + <description>for multiple series and graph types</description> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="2.11.1">fontconfig</requirement> + </requirements> + <command interpreter="bash">r_wrapper.sh $script_file</command> + <configfiles> + <configfile name="script_file"> + ## Setup R error handling to go to stderr + options( show.error.messages=F, + error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + ## Determine range of all series in the plot + xrange = c( NULL, NULL ) + yrange = c( NULL, NULL ) + #for $i, $s in enumerate( $series ) + s${i} = read.table( "${s.input.file_name}", h=${s.header} ) + x${i} = s${i}[,${s.xcol}] + yrange = 0 + #for $column in str($s.ycol).split(','): + y${i}${column} = s${i}[,${column}] + yrange = range(y${i}${column}, yrange, na.rm=TRUE ) + #end for + xrange = range( x${i}, xrange, na.rm=TRUE ) + #end for + ## Open output PDF file + #if $outftype.value == "pdf" + pdf("outfile.pdf") + #else + "${outftype}"( "outfile.${outftype}" , type="cairo") + #end if + ## Dummy plot for axis / labels + plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" ) + ## Plot each series + #for $i, $s in enumerate( $series ) + #if $s.series_type['type'] == "line" + #for $column in str($s.ycol).split(','): + lines( x${i}, y${i}${column}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} ) + #end for + #elif $s.series_type.type == "points" + #for $column in str($s.ycol).split(','): + points( x${i}, y${i}${column}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} ) + #end for + #end if + #end for + ## Close the PDF file + devname = dev.off() + </configfile> + </configfiles> + + <inputs> + <param name="main" type="text" value="" label="Plot Title"/> + <param name="xlab" type="text" value="" label="Label for x axis"/> + <param name="ylab" type="text" value="" label="Label for y axis"/> + <param name="outftype" type="select" label="Output File Type"> + <option value="pdf">PDF</option> + <option value="png">PNG</option> + </param> + <repeat name="series" title="Series"> + <param name="input" type="data" format="tabular" label="Dataset"/> + <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?"/> + <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/> + <param name="ycol" type="data_column" data_ref="input" multiple="true" label="Column for y axis"/> + <conditional name="series_type"> + <param name="type" type="select" label="Series Type"> + <option value="line" selected="true">Line</option> + <option value="points">Points</option> + </param> + <when value="line"> + <param name="lty" type="select" label="Line Type"> + <option value="1">Solid</option> + <option value="2">Dashed</option> + <option value="3">Dotted</option> + </param> + <param name="col" type="select" label="Line Color"> + <option value="1">Black</option> + <option value="2">Red</option> + <option value="3">Green</option> + <option value="4">Blue</option> + <option value="5">Cyan</option> + <option value="6">Magenta</option> + <option value="7">Yellow</option> + <option value="8">Gray</option> + </param> + <param name="lwd" type="float" label="Line Width" value="1.0"/> + </when> + <when value="points"> + <param name="pch" type="select" label="Point Type"> + <option value="1">Circle (hollow)</option> + <option value="2">Triangle (hollow)</option> + <option value="3">Cross</option> + <option value="4">Diamond (hollow)</option> + <option value="15">Square (filled)</option> + <option value="16">Circle (filled)</option> + <option value="17">Triangle (filled)</option> + </param> + <param name="col" type="select" label="Point Color"> + <option value="1">Black</option> + <option value="2">Red</option> + <option value="3">Green</option> + <option value="4">Blue</option> + <option value="5">Cyan</option> + <option value="6">Magenta</option> + <option value="7">Yellow</option> + <option value="8">Gray</option> + </param> + <param name="cex" type="float" label="Point Scale" value="1.0"/> + </when> + </conditional> + </repeat> + </inputs> + <outputs> + <data format="pdf" name="out_file_pdf" from_work_dir="outfile.pdf" > + <filter>(outftype == 'pdf')</filter> + </data> + <data format="png" name="out_file_png" from_work_dir="outfile.png"> + <filter>(outftype == 'png')</filter> + </data> + </outputs> + <tests> + <test> + <param name="main" value="Example XY Plot"/> + <param name="xlab" value="Column 1"/> + <param name="ylab" value="Column 2"/> + <param name="outftype" value="pdf"/> + <param name="input" value="2.tabular" ftype="tabular"/> + <param name="xcol" value="1"/> + <param name="ycol" value="2"/> + <param name="type" value="line"/> + <param name="lty" value="2"/> + <param name="col" value="2"/> + <param name="lwd" value="1.0"/> + <output name="out_file_pdf" file="XY_Plot_1_out.pdf" ftype="pdf" compare="sim_size" /> + </test> + <test><!-- test with file with header line, NA values, multiple ycols and PNG output --> + <param name="main" value="Example XY Plot PNG"/> + <param name="xlab" value="xlab"/> + <param name="ylab" value="ylab"/> + <param name="outftype" value="png"/> + <param name="series_0|input" value="testinput2.tsv" ftype="tabular"/> + <param name="series_0|header" value="TRUE"/> + <param name="series_0|xcol" value="1"/> + <param name="series_0|ycol" value="2,3"/> + <param name="series_0|type" value="points"/> + <param name="series_0|pch" value="1"/> + <param name="series_0|col" value="2"/> + <param name="series_0|cex" value="1.0"/> + <output name="out_file_png" ftype="png" file="testoutput.png" compare="sim_size" /> + </test> + </tests> +<help> +.. class:: infomark + +This tool allows you to plot values contained in columns of a dataset against each other and also allows you to have different series corresponding to the same or different datasets in one plot. + +----- + +.. class:: warningmark + +This tool throws an error if the columns selected for plotting are absent or are not numeric and also if the lengths of these columns differ. + +----- + +**Example** + +Input file:: + + 1 68 4.1 + 2 71 4.6 + 3 62 3.8 + 4 75 4.4 + 5 58 3.2 + 6 60 3.1 + 7 67 3.8 + 8 68 4.1 + 9 71 4.3 + 10 69 3.7 + +Create a two series XY plot on the above data: + +- Series 1: Red Dashed-Line plot between columns 1 and 2 +- Series 2: Blue Circular-Point plot between columns 3 and 2 + +.. image:: xy_example.jpg +</help> +<citations/> +</tool>