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changeset 0:acf952549b53 draft

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Uploaded tool tarball.
author devteam
date Wed, 25 Sep 2013 11:34:32 -0400
parents
children 1a73a2406edc
files r_wrapper.sh test-data/2.tabular test-data/XY_Plot_1_out.pdf tool_dependencies.xml xy_plot.xml
diffstat 5 files changed, 370 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_wrapper.sh	Wed Sep 25 11:34:32 2013 -0400
@@ -0,0 +1,23 @@
+#!/bin/sh
+
+### Run R providing the R script in $1 as standard input and passing 
+### the remaining arguments on the command line
+
+# Function that writes a message to stderr and exits
+function fail
+{
+    echo "$@" >&2
+    exit 1
+}
+
+# Ensure R executable is found
+which R > /dev/null || fail "'R' is required by this tool but was not found on path" 
+
+# Extract first argument
+infile=$1; shift
+
+# Ensure the file exists
+test -f $infile || fail "R input file '$infile' does not exist"
+
+# Invoke R passing file named by first argument to stdin
+R --vanilla --slave $* < $infile
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.tabular	Wed Sep 25 11:34:32 2013 -0400
@@ -0,0 +1,10 @@
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/XY_Plot_1_out.pdf	Wed Sep 25 11:34:32 2013 -0400
@@ -0,0 +1,180 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 25 11:34:32 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="2.11.0">
+        <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xy_plot.xml	Wed Sep 25 11:34:32 2013 -0400
@@ -0,0 +1,151 @@
+<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="" size="30" label="Plot Title"/>
+    <param name="xlab" type="text" value="" size="30" label="Label for x axis"/>
+    <param name="ylab" type="text" value="" size="30" 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:: ${static_path}/images/xy_example.jpg
+</help>
+</tool>