# HG changeset patch
# User bgruening
# Date 1446391621 18000
# Node ID 43a9e7d9b24fa2a4f4a8bd8293100101e9ccceed
# Parent  354d3c6bb894e94f9847fecb743ad7f0a7df716b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty

diff -r 354d3c6bb894 -r 43a9e7d9b24f chemfp_clustering/butina_clustering.xml
--- a/chemfp_clustering/butina_clustering.xml	Thu Aug 15 03:27:06 2013 -0400
+++ b/chemfp_clustering/butina_clustering.xml	Sun Nov 01 10:27:01 2015 -0500
@@ -5,11 +5,13 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command interpreter='python'>
-        butina_clustering.py 
-            -i $infile 
-            -t $threshold 
-            -o $outfile 
+<![CDATA[
+        butina_clustering.py
+            -i $infile
+            -t $threshold
+            -o $outfile
             -p 4
+]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
@@ -26,6 +28,7 @@
         </test>
     </tests>
 <help>
+<![CDATA[
 
 
 .. class:: infomark
@@ -72,10 +75,10 @@
 * Example::
 
 	0 true singletons
-	=> 
+	=>
 
 	0 false singletons
-	=> 
+	=>
 
 	1 clusters
 	55091849 has 12 other members
@@ -91,6 +94,7 @@
 
 .. _chemfp: http://chemfp.com/
 
+]]>
  </help>
 
 </tool>
diff -r 354d3c6bb894 -r 43a9e7d9b24f chemfp_clustering/nxn_clustering.xml
--- a/chemfp_clustering/nxn_clustering.xml	Thu Aug 15 03:27:06 2013 -0400
+++ b/chemfp_clustering/nxn_clustering.xml	Sun Nov 01 10:27:01 2015 -0500
@@ -8,6 +8,7 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command interpreter='python'>
+<![CDATA[
         nxn_clustering.py
             -i $infile
             -t $threshold
@@ -18,6 +19,7 @@
                 --smatrix $smilarity_matrix
             #end if
             --oformat $oformat
+]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
@@ -53,6 +55,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -117,6 +120,7 @@
 
 .. _chemfp: http://chemfp.com/
 
+]]>
     </help>
 
 </tool>
diff -r 354d3c6bb894 -r 43a9e7d9b24f chemfp_mol2fps/mol2fps.xml
--- a/chemfp_mol2fps/mol2fps.xml	Thu Aug 15 03:27:06 2013 -0400
+++ b/chemfp_mol2fps/mol2fps.xml	Sun Nov 01 10:27:01 2015 -0500
@@ -7,6 +7,7 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command>
+<![CDATA[
         #set $fptype = $fp_opts.fp_opts_selector
 
         #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
@@ -44,7 +45,8 @@
                 --substruct
             #end if
         #end if
-        --errors report 2>&#38;1
+        --errors report 2>&1
+]]>
     </command>
     <inputs>
         <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
@@ -165,6 +167,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -186,7 +189,7 @@
 FPS fingerprint file format
 
 * Example::
-	
+
 	      - SDF File
 
 		28434379
@@ -198,7 +201,7 @@
 		    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 
+		    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
@@ -210,28 +213,28 @@
 		  4 18  1  0  0  0  0
 		  ......
 
-			&gt;PUBCHEM_COMPOUND_CID&lt;
+			>PUBCHEM_COMPOUND_CID<
 			28434379
 
-			&gt; &lt;PUBCHEM_COMPOUND_CANONICALIZED&gt;
+			> <PUBCHEM_COMPOUND_CANONICALIZED>
 			1
 
-			&gt; &lt;PUBCHEM_CACTVS_COMPLEXITY&gt;
+			> <PUBCHEM_CACTVS_COMPLEXITY>
 			280
 
-			&gt; &lt;PUBCHEM_CACTVS_HBOND_ACCEPTOR&gt;
+			> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
 			2
 
-			&gt; &lt;PUBCHEM_CACTVS_HBOND_DONOR&gt;
+			> <PUBCHEM_CACTVS_HBOND_DONOR>
 			2
 
-			&gt; &lt;PUBCHEM_CACTVS_ROTATABLE_BOND&gt;
+			> <PUBCHEM_CACTVS_ROTATABLE_BOND>
 			2
 
-			&gt; &lt;PUBCHEM_CACTVS_SUBSKEYS&gt;
+			> <PUBCHEM_CACTVS_SUBSKEYS>
 			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
 
-			&gt;
+			>
 
 		- type : FP2
 
@@ -259,10 +262,10 @@
 
 **Cite**
 
-| `Open Babel`_ 
-| RDKit_ project 
+| `Open Babel`_
+| RDKit_ project
 | chemfp_ project.
-| 
+|
 | N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch and G R Hutchison. `Open Babel: An open chemical toolbox.`_
 
 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
@@ -272,5 +275,6 @@
 .. _`Open Babel`: http://openbabel.org/
 
 
+]]>
     </help>
 </tool>
diff -r 354d3c6bb894 -r 43a9e7d9b24f chemfp_sdf2fps/sdf2fps.xml
--- a/chemfp_sdf2fps/sdf2fps.xml	Thu Aug 15 03:27:06 2013 -0400
+++ b/chemfp_sdf2fps/sdf2fps.xml	Sun Nov 01 10:27:01 2015 -0500
@@ -6,7 +6,9 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command>
+<![CDATA[
         sdf2fps --pubchem "${infile}" > "${outfile}"
+]]>
     </command>
     <inputs>
         <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/>
@@ -17,6 +19,7 @@
     <tests>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -35,7 +38,7 @@
 .. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file
 
 * Example::
-	
+
 		28434379
 		  -OEChem-02031205132D
 
@@ -45,7 +48,7 @@
 		    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 
+		    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
@@ -57,28 +60,28 @@
 		  4 18  1  0  0  0  0
 		  ......
 
-			&gt;PUBCHEM_COMPOUND_CID&lt;
+			>PUBCHEM_COMPOUND_CID<
 			28434379
 
-			&gt; &lt;PUBCHEM_COMPOUND_CANONICALIZED&gt;
+			> <PUBCHEM_COMPOUND_CANONICALIZED>
 			1
 
-			&gt; &lt;PUBCHEM_CACTVS_COMPLEXITY&gt;
+			> <PUBCHEM_CACTVS_COMPLEXITY>
 			280
 
-			&gt; &lt;PUBCHEM_CACTVS_HBOND_ACCEPTOR&gt;
+			> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
 			2
 
-			&gt; &lt;PUBCHEM_CACTVS_HBOND_DONOR&gt;
+			> <PUBCHEM_CACTVS_HBOND_DONOR>
 			2
 
-			&gt; &lt;PUBCHEM_CACTVS_ROTATABLE_BOND&gt;
+			> <PUBCHEM_CACTVS_ROTATABLE_BOND>
 			2
 
-			&gt; &lt;PUBCHEM_CACTVS_SUBSKEYS&gt;
+			> <PUBCHEM_CACTVS_SUBSKEYS>
 			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
 
-			&gt;
+			>
 
 -----
 
@@ -111,5 +114,6 @@
 .. _chemfp: http://chemfp.com/
 
 
+]]>
     </help>
 </tool>
diff -r 354d3c6bb894 -r 43a9e7d9b24f repository_dependencies.xml
--- a/repository_dependencies.xml	Thu Aug 15 03:27:06 2013 -0400
+++ b/repository_dependencies.xml	Sun Nov 01 10:27:01 2015 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format) and the python numpy package.">
-    <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>
diff -r 354d3c6bb894 -r 43a9e7d9b24f tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Aug 15 03:27:06 2013 -0400
+++ b/tool_dependencies.xml	Sun Nov 01 10:27:01 2015 -0500
@@ -1,21 +1,21 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="rdkit" version="2012_12_1">
-        <repository changeset_revision="7c60f011c70c" name="package_rdkit_2012_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="2ab9cdc5cd14" name="package_rdkit_2012_12" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="dddf79f7a6f9" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="chemfp" version="1.1p1">
-        <repository changeset_revision="f2676c09c535" name="package_chemfp_1_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="cb2b38ca9d96" name="package_chemfp_1_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository changeset_revision="aa5180c893f5" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="cfbbe183f8a7" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="openbabel" version="2.3.2">
-        <repository changeset_revision="99a10425de93" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="e5ef70185d24" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>