Mercurial > repos > bgruening > chemfp

diff chemfp_sdf2fps/sdf2fps.xml @ 1:43a9e7d9b24f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
author bgruening
date Sun, 01 Nov 2015 10:27:01 -0500
parents 354d3c6bb894
children
line wrap: on
line diff
--- 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>