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changeset 3:319fa5a9fc1b draft

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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
files r_wrapper.sh test-data/testinput2.tsv test-data/testoutput.png xy_plot.xml
diffstat 4 files changed, 271 insertions(+), 153 deletions(-) [+]
line wrap: on
line diff
--- a/r_wrapper.sh	Fri Oct 09 15:50:24 2015 -0400
+++ b/r_wrapper.sh	Wed Dec 07 18:29:23 2016 -0500
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-### Run R providing the R script in $1 as standard input and passing 
+### Run R providing the R script in $1 as standard input and passing
 ### the remaining arguments on the command line
 
 # Function that writes a message to stderr and exits
@@ -11,7 +11,7 @@
 }
 
 # Ensure R executable is found
-which R > /dev/null || fail "'R' is required by this tool but was not found on path" 
+which R > /dev/null || fail "'R' is required by this tool but was not found on path"
 
 # Extract first argument
 infile=$1; shift
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testinput2.tsv	Wed Dec 07 18:29:23 2016 -0500
@@ -0,0 +1,82 @@
+numsampled	0.03-F3D0	0.03-F3D1
+1	1	1
+100	41.656	45.056
+200	59.033	61.574
+300	70.564	71.47
+400	78.832	78.473
+500	85.365	83.999
+600	90.809	88.67
+700	95.37	92.661
+800	99.424	96.192
+900	102.93	99.322
+1000	106.109	102.104
+1100	109.093	104.719
+1200	111.779	107.177
+1300	114.358	109.452
+1400	116.659	111.602
+1500	118.767	113.489
+1600	120.752	115.256
+1700	122.691	116.981
+1800	124.511	118.561
+1900	126.265	120.041
+2000	127.967	121.466
+2100	129.51	122.863
+2200	130.973	124.201
+2300	132.418	125.504
+2400	133.783	126.659
+2440	134.324	127.108
+2450	134.432	127.22
+2500	135.037	127.781
+2600	136.268	128.837
+2700	137.479	129.829
+2800	138.638	130.799
+2900	139.759	131.741
+3000	140.851	132.618
+3100	141.941	133.494
+3200	142.993	134.339
+3300	144.002	135.161
+3400	144.999	135.897
+3482	145.788	136.509
+3497	145.931	136.616
+3500	145.967	136.635
+3600	146.838	137.341
+3700	147.726	137.99
+3800	148.541	138.637
+3877	149.223	139.149
+3900	149.396	139.3
+4000	150.177	139.985
+4082	150.853	140.463
+4100	150.991	140.575
+4169	151.478	141.019
+4200	151.704	141.206
+4287	152.323	141.704
+4300	152.429	141.784
+4400	153.157	142.358
+4500	153.884	142.945
+4600	154.56	143.523
+4690	155.146	144
+4698	155.195	NA
+4700	155.207	NA
+4800	155.864	NA
+4900	156.501	NA
+5000	157.099	NA
+5100	157.699	NA
+5200	158.304	NA
+5300	158.887	NA
+5315	158.968	NA
+5400	159.501	NA
+5500	160.099	NA
+5582	160.613	NA
+5600	160.709	NA
+5700	161.263	NA
+5773	161.67	NA
+5800	161.81	NA
+5900	162.337	NA
+6000	162.853	NA
+6100	163.362	NA
+6200	163.873	NA
+6223	164	NA
+6300	NA	NA
+6400	NA	NA
+6437	NA	NA
+6500	NA	NA
Binary file test-data/testoutput.png has changed
--- 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>