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changeset 0:36f5fa5bd6d9 draft

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Uploaded
author greg
date Sat, 14 Nov 2015 14:06:46 -0500
parents
children e3350521105e
files icqsol_compose_shapes.py icqsol_compose_shapes.xml icqsol_macros.xml icqsol_utils.py test-data/head.vtkascii test-data/notch1.vtkascii test-data/notch2.vtkascii test-data/philips_bolt.vtkascii test-data/shaft.vtkascii tool_dependencies.xml
diffstat 10 files changed, 1280 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_compose_shapes.py	Sat Nov 14 14:06:46 2015 -0500
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+import argparse
+import shutil
+
+import icqsol_utils
+from icqsol.shapes.icqShapeManager import ShapeManager
+
+# Parse Command Line.
+parser = argparse.ArgumentParser()
+parser.add_argument( '--expression', dest='expression', help='Composition expression' )
+parser.add_argument( '--shape_dataset', dest='shape_datasets', action='append', nargs=4, help='Shape datasets selected from history' )
+parser.add_argument( '--output', dest='output', help='Output dataset' )
+parser.add_argument( '--output_vtk_type', dest='output_vtk_type', help='Output file format and type' )
+
+args = parser.parse_args()
+
+tmp_dir = icqsol_utils.get_temp_dir()
+shape_tuples = []
+shape_mgr = ShapeManager()
+
+# Load the shapes.
+for ( expression_var, dataset_path, galaxy_ext, vtk_dataset_type ) in args.shape_datasets:
+    # Define the file format and type.
+    format, file_type = icqsol_utils.get_format_and_type( galaxy_ext )
+    if format == 'vtk':
+        shape_mgr.setReader( file_format=format, vtk_dataset_type=vtk_dataset_type )
+    else:
+        shape_mgr.setReader( file_format=format )
+    icqsol_path = icqsol_utils.get_input_file_path( tmp_dir, dataset_path, format )
+    shape_tuple = ( expression_var, shape_mgr.loadAsShape( icqsol_path ) )
+    shape_tuples.append( shape_tuple )
+
+# Define the output file format and type.
+output_format, output_file_type = icqsol_utils.get_format_and_type( args.output_vtk_type )
+tmp_output_path = icqsol_utils.get_temporary_file_path( tmp_dir, output_format )
+
+shape_mgr.setWriter( file_format=output_format, vtk_dataset_type=icqsol_utils.POLYDATA )
+
+# Compose the shapes.
+composite_shape = shape_mgr.composeShapes( shape_tuples, args.expression )
+
+# Save the output.
+shape_mgr.saveShape( shape=composite_shape, file_name=tmp_output_path, file_type=output_file_type )
+shutil.move( tmp_output_path, args.output )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_compose_shapes.xml	Sat Nov 14 14:06:46 2015 -0500
@@ -0,0 +1,76 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="icqsol_compose_shapes" name="Compose 3D shapes" version="1.0.0">
+    <description></description>
+    <macros>
+        <import>icqsol_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/icqsol_compose_shapes.py
+    --expression "$expression"
+    #for $i in $input_shapes:
+        --shape_dataset "${i.expression_var}" "${i.input_shape}" "${i.input_shape.ext}" "${i.input_shape.metadata.dataset_type}"
+    #end for
+    --output "$output"
+    --output_vtk_type $output_vtk_type
+]]>
+    </command>
+    <inputs>
+        <param name="expression" type="text" value="" label="Composition expression" help="Example: A + B - C * D"/>
+        <repeat name="input_shapes" title="Expression variable and shape" min="2">
+            <param name="expression_var" type="text" value="" label="Expression variable" help="The selected shape will be associated with this variable in the expression."/>
+            <param name="input_shape" type="data" format="plyascii,plybinary,vtkascii,vtkbinary" label="Shape">
+                <validator type="dataset_ok_validator" />
+            </param>
+        </repeat>
+        <expand macro="output_vtk_type_params" />
+    </inputs>
+    <outputs>
+        <data name="output" format="vtkascii" label="${tool.name} ${on_string}">
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="output_vtk_type" />
+                </action>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="expression" value="head + shaft - notch1 - notch2" />
+            <repeat name="input_shapes">
+                <param name="expression_var" value="head" />
+                <param name="input_shape" value="head.vtkascii" ftype="vtkascii" />
+            </repeat>
+            <repeat name="input_shapes">
+                <param name="expression_var" value="shaft" />
+                <param name="input_shape" value="shaft.vtkascii" ftype="vtkascii" />
+            </repeat>
+            <repeat name="input_shapes">
+                <param name="expression_var" value="notch1" />
+                <param name="input_shape" value="notch1.vtkascii" ftype="vtkascii" />
+            </repeat>
+            <repeat name="input_shapes">
+                <param name="expression_var" value="notch2" />
+                <param name="input_shape" value="notch2.vtkascii" ftype="vtkascii" />
+            </repeat>
+            <output name="output" file="philips_bolt.vtkascii" ftype="vtkascii" />
+            <param name="output_vtk_type" value="vtkascii" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+<![CDATA[
+Creates a shape composed of any number of selected shapes where the composition is based on a mathematical
+expression consisting of **+**, **-** and ***** operations.  The **+** results in a union of shapes, the
+**-** operator removes a shape and the ***** operator results in an intersection of shapes.
+
+For example, if the **Composition expression** is **A + B - C - D**, selecting 4 shapes from your history
+and associating each shape with a variable from the expression will result in a shape composed of the shapes
+associated with A and B, but eliminating the shapes associated with C and D.
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_macros.xml	Sat Nov 14 14:06:46 2015 -0500
@@ -0,0 +1,115 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.0">icqsol</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:"/>
+            <exit_code range=":-1"/>
+            <regex match="Error:"/>
+            <regex match="Exception:"/>
+        </stdio>
+    </xml>
+    <!-- TODO: place this in colormaps_conf.xml -->
+    <xml name="color_map_param">
+        <param name="color_map" type="select" label="Color map">
+            <option value="hot" selected="True">Hot</option>
+            <option value="cold">Cold</option>
+            <option value="blackbody">Blackbody</option>
+            <option value="gnu">Gnu</option>
+        </param>
+    </xml>
+    <xml name="output_vtk_type_params">
+        <param name="output_vtk_type" type="select" label="Output file type">
+            <option value="vtkascii" selected="True">Vtk-ascii</option>
+            <option value="vtkbinary">Vtk-binary</option>
+        </param>
+    </xml>
+    <token name="@origin_cmd_args@">
+        --origin_x $create_process_cond.shape_cond.origin_x
+        --origin_y $create_process_cond.shape_cond.origin_y
+        --origin_z $create_process_cond.shape_cond.origin_z
+    </token>
+    <xml name="origin_params">
+        <param name="origin_x" type="float" value="0.0" label="X coordinate of origin" help="Floating point number"/>
+        <param name="origin_y" type="float" value="0.0" label="Y coordinate of origin" help="Floating point number"/>
+        <param name="origin_z" type="float" value="0.0" label="Z coordinate of origin" help="Floating point number"/>
+    </xml>
+    <token name="@lengths_cmd_args@">
+        --length_x $create_process_cond.shape_cond.length_x
+        --length_y $create_process_cond.shape_cond.length_y
+        --length_z $create_process_cond.shape_cond.length_z
+    </token>
+    <xml name="lengths_params">
+        <!-- At least one of these lengths must be greater than zero, but we have no validator for this. -->
+        <param name="length_x" type="float" value="1.0" label="Length in the X direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="false" />
+        </param>
+        <param name="length_y" type="float" value="0.0" label="Length in the Y direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="false" />
+        </param>
+        <param name="length_z" type="float" value="0.0" label="Length in the Z direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="false" />
+        </param>
+    </xml>
+    <xml name="lengths_exclude_min_params">
+        <param name="length_x" type="float" value="1.0" label="Length in the X direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="true" />
+        </param>
+        <param name="length_y" type="float" value="1.0" label="Length in the Y direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="true" />
+        </param>
+        <param name="length_z" type="float" value="1.0" label="Length in the Z direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="true" />
+        </param>
+    </xml>
+    <token name="@radius_cmd_args@">
+        --radius $create_process_cond.shape_cond.radius
+    </token>
+    <xml name="radius_params">
+        <param name="radius" type="float" value="1.0" label="Radius" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="True" />
+        </param>
+    </xml>
+    <token name="@n_theta_cmd_args@">
+        --n_theta $create_process_cond.shape_cond.n_theta
+    </token>
+    <xml name="n_theta_params">
+        <param name="n_theta" type="integer" value="16" label="Number of slices" help="Controls the tessellation along the longitude direction">
+            <validator type="in_range" min="0" exclude_min="False" />
+        </param>
+    </xml>
+    <token name="@n_phi_cmd_args@">
+        --n_phi $create_process_cond.shape_cond.n_phi
+    </token>
+    <xml name="n_phi_params">
+        <param name="n_phi" type="integer" value="8" label="Number of stacks" help="Controls the tessellation along the latitude direction">
+            <validator type="in_range" min="0" exclude_min="False" />
+        </param>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @unpublished{None,
+                author = {None},
+                title = {None},
+                year = {None},
+                eprint = {None},
+                url = {https://github.com/gregvonkuster/galaxy-csg}
+            }</citation>
+            <citation type="bibtex">
+                @misc(Schroeder-Martin-Lorensen2006,
+                author = "Will Schroeder and 
+                          Ken Martin and
+                          Bill Lorensen",
+                year = "2006",
+                title = "The Visualization Toolkit (4th ed.)",
+                publisher =  "Kitware",
+                url = "https://en.wikipedia.org/wiki/Special:BookSources/978-1-930934-19-1")
+            </citation>
+        </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_utils.py	Sat Nov 14 14:06:46 2015 -0500
@@ -0,0 +1,59 @@
+import os
+import sys
+import tempfile
+
+POLYDATA='POLYDATA'
+
+def asbool( val ):
+    return str( val ).lower() in [ 'yes', 'true' ]
+
+def get_format_and_type( galaxy_ext ):
+    # Define the output file format and type.
+    format = None
+    datatype = None
+    if galaxy_ext in [ 'vtkascii', 'vtkbinary' ]:
+        format = 'vtk'
+    elif galaxy_ext in [ 'plyascii', 'plybinary' ]:
+        format = 'ply'
+    if galaxy_ext in [ 'vtkascii', 'plyascii' ]:
+        datatype = 'ascii'
+    elif galaxy_ext in [ 'vtkbinary', 'plybinary' ]:
+        datatype = 'binary'
+    return format, datatype
+
+def get_input_file_path( tmp_dir, input_file, format ):
+    """
+    iCqSol uses file extensions (e.g., .ply, .vtk) when reading and
+    writing files, so the Galaxy dataset naming convention of
+    setting all file extensions as .dat must be handled.
+    """
+    file_path = get_temporary_file_path( tmp_dir, format )
+    # Remove the file so we can create a symlink.
+    os.remove( file_path )
+    os.symlink( input_file, file_path )
+    return file_path
+
+def get_temp_dir( prefix='tmp-vtk-', dir=None ):
+    """
+    Return a temporary directory.
+    """
+    return tempfile.mkdtemp( prefix=prefix, dir=dir )
+
+def get_tempfilename( dir=None, suffix=None ):
+    """
+    Return a temporary file name.
+    """
+    fd, name = tempfile.mkstemp( suffix=suffix, dir=dir )
+    os.close( fd )
+    return name
+
+def get_temporary_file_path( tmp_dir, file_extension ):
+    """
+    Return the path to a temporary file with a valid VTK format
+    file extension.
+    """
+    return get_tempfilename( tmp_dir, file_extension )
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/head.vtkascii	Sat Nov 14 14:06:46 2015 -0500
@@ -0,0 +1,65 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 34 float
+-0.06 0 0 -0.06 0 -0.25 -0.06 -0.0956709 -0.23097 
+0.08 0 0 -0.06 -0.176777 -0.176777 -0.06 -0.23097 -0.0956709 
+-0.06 -0.25 -1.53081e-17 -0.06 -0.23097 0.0956709 -0.06 -0.176777 0.176777 
+-0.06 -0.0956709 0.23097 -0.06 -3.06162e-17 0.25 -0.06 0.0956709 0.23097 
+-0.06 0.176777 0.176777 -0.06 0.23097 0.0956709 -0.06 0.25 4.59243e-17 
+-0.06 0.23097 -0.0956709 -0.06 0.176777 -0.176777 -0.06 0.0956709 -0.23097 
+-0.06 0 -0.25 -0.06 -0.0956709 -0.23097 -0.06 -0.176777 -0.176777 
+-0.06 -0.23097 -0.0956709 -0.06 -0.25 -1.53081e-17 -0.06 -0.23097 0.0956709 
+-0.06 -0.176777 0.176777 -0.06 -0.0956709 0.23097 -0.06 -3.06162e-17 0.25 
+-0.06 0.0956709 0.23097 -0.06 0.176777 0.176777 -0.06 0.23097 0.0956709 
+-0.06 0.25 4.59243e-17 -0.06 0.23097 -0.0956709 -0.06 0.176777 -0.176777 
+-0.06 0.0956709 -0.23097 
+POLYGONS 32 128
+3 0 1 2 
+3 18 3 19 
+3 0 2 4 
+3 19 3 20 
+3 0 4 5 
+3 20 3 21 
+3 0 5 6 
+3 21 3 22 
+3 0 6 7 
+3 22 3 23 
+3 0 7 8 
+3 23 3 24 
+3 0 8 9 
+3 24 3 25 
+3 0 9 10 
+3 25 3 26 
+3 0 10 11 
+3 26 3 27 
+3 0 11 12 
+3 27 3 28 
+3 0 12 13 
+3 28 3 29 
+3 0 13 14 
+3 29 3 30 
+3 0 14 15 
+3 30 3 31 
+3 0 15 16 
+3 31 3 32 
+3 0 16 17 
+3 32 3 33 
+3 0 17 1 
+3 33 3 18 
+
+POINT_DATA 34
+NORMALS Normals float
+-1 0 0 -1 0 0 -1 0 0 
+1 2.30575e-08 6.43464e-09 -1 0 0 -1 0 0 
+-1 0 0 -1 0 0 -1 0 0 
+-1 0 0 -1 0 0 -1 0 0 
+-1 0 0 -1 0 0 -1 0 0 
+-1 0 0 -1 0 0 -1 0 0 
+0.872506 0 -0.488603 0.872506 -0.18698 -0.451411 0.872506 -0.345495 -0.345495 
+0.872506 -0.451411 -0.18698 0.872506 -0.488603 0 0.872506 -0.451411 0.18698 
+0.872506 -0.345495 0.345495 0.872506 -0.18698 0.451411 0.872506 0 0.488603 
+0.872506 0.18698 0.451411 0.872506 0.345495 0.345495 0.872506 0.451411 0.18698 
+0.872506 0.488603 0 0.872506 0.451411 -0.18698 0.872506 0.345495 -0.345495 
+0.872506 0.18698 -0.451411 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/notch1.vtkascii	Sat Nov 14 14:06:46 2015 -0500
@@ -0,0 +1,33 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 24 float
+-0.06 -0.015 -0.15 -0.06 -0.015 0.15 -0.06 0.015 0.15 
+-0.06 0.015 -0.15 -0.03 -0.015 -0.15 -0.03 0.015 -0.15 
+-0.03 0.015 0.15 -0.03 -0.015 0.15 -0.06 -0.015 -0.15 
+-0.06 -0.015 -0.15 -0.06 -0.015 0.15 -0.06 -0.015 0.15 
+-0.06 0.015 0.15 -0.06 0.015 0.15 -0.06 0.015 -0.15 
+-0.06 0.015 -0.15 -0.03 -0.015 -0.15 -0.03 -0.015 -0.15 
+-0.03 0.015 -0.15 -0.03 0.015 -0.15 -0.03 0.015 0.15 
+-0.03 0.015 0.15 -0.03 -0.015 0.15 -0.03 -0.015 0.15 
+
+POLYGONS 6 30
+4 0 1 2 3 
+4 4 5 6 7 
+4 8 16 22 10 
+4 14 12 20 18 
+4 9 15 19 17 
+4 11 23 21 13 
+
+POINT_DATA 24
+NORMALS Normals float
+-1 0 0 -1 0 0 -1 0 0 
+-1 0 0 1 0 0 1 0 0 
+1 0 0 1 0 0 0 -1 0 
+0 0 -1 0 -1 0 0 0 1 
+0 1 0 0 0 1 0 1 0 
+0 0 -1 0 -1 0 0 0 -1 
+0 1 0 0 0 -1 0 1 0 
+0 0 1 0 -1 0 0 0 1 
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/notch2.vtkascii	Sat Nov 14 14:06:46 2015 -0500
@@ -0,0 +1,33 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 24 float
+-0.06 -0.15 0.015 -0.06 0.15 0.015 -0.06 0.15 -0.015 
+-0.06 -0.15 -0.015 -0.03 -0.15 0.015 -0.03 -0.15 -0.015 
+-0.03 0.15 -0.015 -0.03 0.15 0.015 -0.06 -0.15 0.015 
+-0.06 -0.15 0.015 -0.06 0.15 0.015 -0.06 0.15 0.015 
+-0.06 0.15 -0.015 -0.06 0.15 -0.015 -0.06 -0.15 -0.015 
+-0.06 -0.15 -0.015 -0.03 -0.15 0.015 -0.03 -0.15 0.015 
+-0.03 -0.15 -0.015 -0.03 -0.15 -0.015 -0.03 0.15 -0.015 
+-0.03 0.15 -0.015 -0.03 0.15 0.015 -0.03 0.15 0.015 
+
+POLYGONS 6 30
+4 0 1 2 3 
+4 4 5 6 7 
+4 8 16 22 10 
+4 14 12 20 18 
+4 9 15 19 17 
+4 11 23 21 13 
+
+POINT_DATA 24
+NORMALS Normals float
+-1 0 0 -1 0 0 -1 0 0 
+-1 0 0 1 0 0 1 0 0 
+1 0 0 1 0 0 0 0 1 
+0 -1 0 0 0 1 0 1 0 
+0 0 -1 0 1 0 0 0 -1 
+0 -1 0 0 0 1 0 -1 0 
+0 0 -1 0 -1 0 0 0 -1 
+0 1 0 0 0 1 0 1 0 
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/philips_bolt.vtkascii	Sat Nov 14 14:06:46 2015 -0500
@@ -0,0 +1,746 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 674 float
+-0.06 -0.0362132 0.015 -0.06 -0.247016 0.015 -0.06 -0.23097 0.0956709 
+-0.06 -0.015 0.015 -0.06 -0.0362132 0.015 -0.06 -0.176777 0.176777 
+-0.06 -0.015 0.0362132 -0.06 -0.0956709 0.23097 -0.06 -0.015 0.0362132 
+-0.06 -0.015 0.247016 -0.06 0.015 0.0362132 -0.06 0.015 0.247016 
+-0.06 0.0956709 0.23097 -0.06 0.015 0.015 -0.06 0.015 0.0362132 
+-0.06 0.176777 0.176777 -0.06 0.0362132 0.015 -0.06 0.23097 0.0956709 
+-0.06 0.0362132 0.015 -0.06 0.247016 0.015 -0.06 -1.83697e-17 0.15 
+-0.06 -0.015 0.15 -0.06 -3.06162e-17 0.25 -0.06 0.015 0.15 
+-0.06 -0.015 -0.0362132 -0.06 -0.015 -0.247016 -0.06 -0.0956709 -0.23097 
+-0.06 -0.015 -0.015 -0.06 -0.015 -0.0362132 -0.06 -0.176777 -0.176777 
+-0.06 -0.0362132 -0.015 -0.06 -0.23097 -0.0956709 -0.06 -0.0362132 -0.015 
+-0.06 -0.247016 -0.015 -0.06 0.0362132 -0.015 -0.06 0.247016 -0.015 
+-0.06 0.23097 -0.0956709 -0.06 0.015 -0.015 -0.06 0.0362132 -0.015 
+-0.06 0.176777 -0.176777 -0.06 0.015 -0.0362132 -0.06 0.0956709 -0.23097 
+-0.06 0.015 -0.0362132 -0.06 0.015 -0.247016 -0.06 -0.015 -0.15 
+-0.06 0 -0.15 -0.06 0 -0.25 -0.06 0.015 -0.15 
+-0.06 -0.15 -9.18486e-18 -0.06 -0.15 -0.015 -0.06 -0.25 -1.53081e-17 
+-0.06 -0.15 0.015 -0.06 0.15 2.75546e-17 -0.06 0.15 0.015 
+-0.06 0.25 4.59243e-17 -0.06 0.15 -0.015 -0.03 -0.1 -5.37764e-17 
+-0.03 -0.0970163 0.015 -0.03 -0.015 0.015 -0.03 -0.015 -0.015 
+-0.03 -0.0970163 -0.015 -0.03 3.64292e-17 -0.1 -0.03 -0.015 -0.0970163 
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shaft.vtkascii	Sat Nov 14 14:06:46 2015 -0500
@@ -0,0 +1,103 @@
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+vtk output
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Nov 14 14:06:46 2015 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="icqsol" version="1.0">
+        <repository changeset_revision="a357536fb363" name="package_icqsol_1_0" owner="greg" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>