Mercurial > repos > bgruening > chemfp

changeset 9:18617b9fc70e

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Sat, 11 May 2013 17:12:34 -0400
parents d241ff83e485
children 4b5cb4328146
files chemfp_mol2fps/mol2fps.xml chemfp_mol2fps/ob2fps.xml repository_dependencies.xml tool_dependencies.xml
diffstat 4 files changed, 244 insertions(+), 244 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/mol2fps.xml	Sat May 11 17:12:34 2013 -0400
@@ -0,0 +1,239 @@
+<tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.2.0">
+    <description>with different fingerprint types</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+        <requirement type="package" version="2012_12_1">rdkit</requirement>
+    </requirements>
+    <command>
+        #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
+            ## Open Babel fingerprints
+            ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&#38;1
+        #else:
+            ## RDKit fingerprints
+            rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}"
+            #if $fp_opts.fp_opts_selector=="--RDK":
+                --RDK
+                --fpSize $fp_opts.fpSize
+                --minPath $fp_opts.minPath
+                --maxPath $fp_opts.maxPath
+                --nBitsPerHash $fp_opts.nBitsPerHash
+                $fp_opts.useHs
+            #elif $fp_opts.fp_opts_selector=="--torsions":
+                --torsions
+                --fpSize $fp_opts.fpSize
+                --targetSize $fp_opts.targetSize
+            #elif $fp_opts.fp_opts_selector=="--morgan":
+                --morgan
+                --fpSize $fp_opts.fpSize
+                --radius $fp_opts.radius
+                $fp_opts.useFeatures
+                $fp_opts.useChirality
+                $fp_opts.useBondTypes
+            #elif $fp_opts.fp_opts_selector=="--pairs":
+                --paris
+                --fpSize $fp_opts.fpSize
+                --minLength $fp_opts.minLength
+                --maxLength $fp_opts.maxLength
+            #elif $fp_opts.fp_opts_selector=="--maccs166":
+                --maccs166
+            #elif $fp_opts.fp_opts_selector=="--substruct":
+                --substruct
+            #endif
+            --errors report 2>&#38;1
+        #endif
+    </command>
+    <inputs>
+        <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
+        <conditional name="fp_opts">
+            <param name="fp_opts_selector" type="select" label="Type of fingerprint">
+                <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option>
+                <option value='--FP3'>Open Babel FP3 fingerprints</option>
+                <option value='--FP4'>Open Babel FP4 fingerprints</option>
+                <option value='--MACCS'>Open Babel MACCS fingerprints</option>
+                <option value='--RDK'>RDKit topological fingerprint</option>
+                <option value='--torsions'>RDKit topological Torsion fingerprints</option>
+                <option value='--morgan'>RDKit Morgan fingerprints</option>
+                <option value='--pairs'>RDKit Atom Pair fingerprints</option>
+                <option value='--maccs166'>RDKit MACCS fingerprints</option>
+                <option value='--substruct'>RDKit substructure fingerprints</option>
+            </param>
+            <when value="--FP2" />
+            <when value="--FP3" />
+            <when value="--FP4" />
+            <when value="--MACCS" />
+            <when value="--RDK">
+                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+                <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+                <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+                <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+                <param name="useHs" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" />
+            </when>
+            <when value="--torsions">
+                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+                <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+            </when>
+            <when value="--morgan">
+                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+                <param name="radius" type="integer" value="2" label="radius for the Morgan algorithm" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+                <param name="useFeatures" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false" />
+                <param name="useChirality" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false" />
+                <param name="useBondTypes" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true" />
+            </when>
+            <when value="--pairs">
+                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+                <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+                <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help="">
+                    <validator type="in_range" min="1" />
+                </param>
+            </when>
+            <when value="--maccs166" />
+            <when value="--substruct" />
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fps" />
+    </outputs>
+    <tests>
+        <!-- FP2 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--FP2" />
+            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--FP2" />
+            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
+        </test>
+        <!-- FP3 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--FP3" />
+            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--FP3" />
+            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
+        </test>
+        <!-- FP4 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--FP4" />
+            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--FP4" />
+            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
+        </test>
+        <!-- MACCS -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--MACCS" />
+            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--MACCS" />
+            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
+        </test>
+    </tests>
+    <help>
+
+
+**What it does**
+
+Generate fingerprints using OpenBabel
+
+-----
+
+**Example**
+
+* input::
+	
+	      - SDF File
+
+		28434379
+		  -OEChem-02031205132D
+
+		 37 39  0     0  0  0  0  0  0999 V2000
+		    8.1648   -1.8842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.0812   -0.2134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.0812   -1.8229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    2.5369   -2.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.3919    0.7371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+		    7.3704    0.9433    0.0000 C   0  0  0  0 
+		    ......
+		  1 15  1  0  0  0  0
+		  1 35  1  0  0  0  0
+		  2  5  1  0  0  0  0
+		  2 11  1  0  0  0  0
+		  2 12  1  0  0  0  0
+		  3 12  2  0  0  0  0
+		  3 13  1  0  0  0  0
+		  4 18  1  0  0  0  0
+		  ......
+
+			&gt;PUBCHEM_COMPOUND_CID&lt;
+			28434379
+
+			&gt; &lt;PUBCHEM_COMPOUND_CANONICALIZED&gt;
+			1
+
+			&gt; &lt;PUBCHEM_CACTVS_COMPLEXITY&gt;
+			280
+
+			&gt; &lt;PUBCHEM_CACTVS_HBOND_ACCEPTOR&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_HBOND_DONOR&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_ROTATABLE_BOND&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_SUBSKEYS&gt;
+			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
+
+			&gt;
+
+		- type : FP2
+
+* output::
+
+	#FPS1
+	#num_bits=1021
+	#type=OpenBabel-FP2/1
+	#software=OpenBabel/2.3.0
+	#source=/tmp/dataset_409.dat.sdf
+	#date=2012-02-03T11:13:39
+	c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
+	0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
+	10000000000080000000c0000060000c0000060810000010000000800102000000	28434379
+
+
+    </help>
+</tool>
--- a/chemfp_mol2fps/ob2fps.xml	Fri Apr 26 11:07:08 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,239 +0,0 @@
-<tool id="chemfp_mol2fps" name="Molecules to Fingerprints" version="0.2.0">
-    <description>with different fingerprint types</description>
-    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
-    <requirements>
-        <requirement type="package" version="1.1p1">chemfp</requirement>
-        <requirement type="package" version="2012_12_1">rdkit</requirement>
-    </requirements>
-    <command>
-        #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
-            ## Open Babel fingerprints
-            ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&#38;1
-        #else:
-            ## RDKit fingerprints
-            rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}"
-            #if $fp_opts.fp_opts_selector=="--RDK":
-                --RDK
-                --fpSize $fp_opts.fpSize
-                --minPath $fp_opts.minPath
-                --maxPath $fp_opts.maxPath
-                --nBitsPerHash $fp_opts.nBitsPerHash
-                $fp_opts.useHs
-            #elif $fp_opts.fp_opts_selector=="--torsions":
-                --torsions
-                --fpSize $fp_opts.fpSize
-                --targetSize $fp_opts.targetSize
-            #elif $fp_opts.fp_opts_selector=="--morgan":
-                --morgan
-                --fpSize $fp_opts.fpSize
-                --radius $fp_opts.radius
-                $fp_opts.useFeatures
-                $fp_opts.useChirality
-                $fp_opts.useBondTypes
-            #elif $fp_opts.fp_opts_selector=="--pairs":
-                --paris
-                --fpSize $fp_opts.fpSize
-                --minLength $fp_opts.minLength
-                --maxLength $fp_opts.maxLength
-            #elif $fp_opts.fp_opts_selector=="--maccs166":
-                --maccs166
-            #elif $fp_opts.fp_opts_selector=="--substruct":
-                --substruct
-            #endif
-            --errors report 2>&#38;1
-        #endif
-    </command>
-    <inputs>
-        <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
-        <conditional name="fp_opts">
-            <param name="fp_opts_selector" type="select" label="Type of fingerprint">
-                <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option>
-                <option value='--FP3'>Open Babel FP3 fingerprints</option>
-                <option value='--FP4'>Open Babel FP4 fingerprints</option>
-                <option value='--MACCS'>Open Babel MACCS fingerprints</option>
-                <option value='--RDK'>RDKit topological fingerprint</option>
-                <option value='--torsions'>RDKit topological Torsion fingerprints</option>
-                <option value='--morgan'>RDKit Morgan fingerprints</option>
-                <option value='--pairs'>RDKit Atom Pair fingerprints</option>
-                <option value='--maccs166'>RDKit MACCS fingerprints</option>
-                <option value='--substruct'>RDKit substructure fingerprints</option>
-            </param>
-            <when value="--FP2" />
-            <when value="--FP3" />
-            <when value="--FP4" />
-            <when value="--MACCS" />
-            <when value="--RDK">
-                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="useHs" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" />
-            </when>
-            <when value="--torsions">
-                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-            </when>
-            <when value="--morgan">
-                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="radius" type="integer" value="2" label="radius for the Morgan algorithm" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="useFeatures" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false" />
-                <param name="useChirality" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false" />
-                <param name="useBondTypes" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true" />
-            </when>
-            <when value="--pairs">
-                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-            </when>
-            <when value="--maccs166" />
-            <when value="--substruct" />
-        </conditional>
-
-    </inputs>
-    <outputs>
-        <data name="outfile" format="fps" />
-    </outputs>
-    <tests>
-        <!-- FP2 -->
-        <test>
-            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
-            <param name="fptype" value="--FP2" />
-            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
-        </test>
-        <test>
-            <param name="infile" value="CID_2244.smi" ftype="smi" />
-            <param name="fptype" value="--FP2" />
-            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
-        </test>
-        <!-- FP3 -->
-        <test>
-            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
-            <param name="fptype" value="--FP3" />
-            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
-        </test>
-        <test>
-            <param name="infile" value="CID_2244.smi" ftype="smi" />
-            <param name="fptype" value="--FP3" />
-            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
-        </test>
-        <!-- FP4 -->
-        <test>
-            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
-            <param name="fptype" value="--FP4" />
-            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
-        </test>
-        <test>
-            <param name="infile" value="CID_2244.smi" ftype="smi" />
-            <param name="fptype" value="--FP4" />
-            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
-        </test>
-        <!-- MACCS -->
-        <test>
-            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
-            <param name="fptype" value="--MACCS" />
-            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
-        </test>
-        <test>
-            <param name="infile" value="CID_2244.smi" ftype="smi" />
-            <param name="fptype" value="--MACCS" />
-            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
-        </test>
-    </tests>
-    <help>
-
-
-**What it does**
-
-Generate fingerprints using OpenBabel
-
------
-
-**Example**
-
-* input::
-	
-	      - SDF File
-
-		28434379
-		  -OEChem-02031205132D
-
-		 37 39  0     0  0  0  0  0  0999 V2000
-		    8.1648   -1.8842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-		    6.0812   -0.2134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
-		    6.0812   -1.8229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
-		    2.5369   -2.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
-		    6.3919    0.7371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-		    7.3704    0.9433    0.0000 C   0  0  0  0 
-		    ......
-		  1 15  1  0  0  0  0
-		  1 35  1  0  0  0  0
-		  2  5  1  0  0  0  0
-		  2 11  1  0  0  0  0
-		  2 12  1  0  0  0  0
-		  3 12  2  0  0  0  0
-		  3 13  1  0  0  0  0
-		  4 18  1  0  0  0  0
-		  ......
-
-			&gt;PUBCHEM_COMPOUND_CID&lt;
-			28434379
-
-			&gt; &lt;PUBCHEM_COMPOUND_CANONICALIZED&gt;
-			1
-
-			&gt; &lt;PUBCHEM_CACTVS_COMPLEXITY&gt;
-			280
-
-			&gt; &lt;PUBCHEM_CACTVS_HBOND_ACCEPTOR&gt;
-			2
-
-			&gt; &lt;PUBCHEM_CACTVS_HBOND_DONOR&gt;
-			2
-
-			&gt; &lt;PUBCHEM_CACTVS_ROTATABLE_BOND&gt;
-			2
-
-			&gt; &lt;PUBCHEM_CACTVS_SUBSKEYS&gt;
-			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
-
-			&gt;
-
-		- type : FP2
-
-* output::
-
-	#FPS1
-	#num_bits=1021
-	#type=OpenBabel-FP2/1
-	#software=OpenBabel/2.3.0
-	#source=/tmp/dataset_409.dat.sdf
-	#date=2012-02-03T11:13:39
-	c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
-	0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
-	10000000000080000000c0000060000c0000060810000010000000800102000000	28434379
-
-
-    </help>
-</tool>
--- a/repository_dependencies.xml	Fri Apr 26 11:07:08 2013 -0400
+++ b/repository_dependencies.xml	Sat May 11 17:12:34 2013 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format) and the python numpy package.">
-    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="e533de975501" />
-    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="c3041382815c" />
+    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="1a070566e9c6" />
+    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="ec80bba4bccb" />
 </repositories>
--- a/tool_dependencies.xml	Fri Apr 26 11:07:08 2013 -0400
+++ b/tool_dependencies.xml	Sat May 11 17:12:34 2013 -0400
@@ -1,12 +1,12 @@
 <tool_dependency>
     <package name="rdkit" version="2012_12_1">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_rdkit_2012_12" owner="bgruening" changeset_revision="0adc830e7d71" />
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_rdkit_2012_12" owner="bgruening" changeset_revision="158956be0623" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="c3041382815c" />
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="ec80bba4bccb" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_matplotlib_1_2" owner="bgruening" changeset_revision="ae165d9e610a" />
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_matplotlib_1_2" owner="bgruening" changeset_revision="f2c19c75befd" />
     </package>
 
     <package name="chemfp" version="1.1p1">