# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1370195691 -7200
# Node ID 47d2bf6919081343955b0ecde25c797315c8b085
# Parent  dbe9c82028d17505d06b49f57ca625e984688ed1
ChemicalToolBoX update.

diff -r dbe9c82028d1 -r 47d2bf691908 simsearch.xml
--- a/simsearch.xml	Sat Jun 01 20:03:57 2013 +0200
+++ b/simsearch.xml	Sun Jun 02 19:54:51 2013 +0200
@@ -6,17 +6,19 @@
     </requirements>
     <command>
         #if $method_opts.method_opts_selector == "chemfp":
-            ## TODO: remove all comment lines, in muti mode many comment lines will be appear, also in the middle of the result file, remove them
-            #if int($method_opts.knn) == 0:
-                #set $k = 'all'
-            #else:
-                #set $k = int($method_opts.knn)
-            #end if
             simsearch 
+                #if int($method_opts.knn) == 0:
+                    #set $k = 'all'
+                    ## count is only available if k nearest neighbor search is disabled
+                    $method_opts.counts
+                #else:
+                    #set $k = int($method_opts.knn)
+                #end if
+
                 -k $k 
-                --threshold $method_opts.threshold 
-                --query-format fps 
-                $method_opts.counts
+
+                --threshold $method_opts.threshold
+                --query-format fps
                 --target-format fps
                 -o "${outfile}"
 
@@ -67,8 +69,8 @@
                 <param name='knn' type='integer' value='0' label='select the k nearest neighbors' help='0 means all neighbors'>
                    <validator type="in_range" min="0" />
                 </param>
-                <param name='threshold' type='float' label='threshold' value='0.7'/>
-                <param name="counts" type="boolean" label="report counts (-c)" truevalue="-c" falsevalue="" checked="false" />
+                <param name='threshold' type='float' value='0.7' label='threshold' />
+                <param name="counts" type="boolean" truevalue="-c" falsevalue="" checked="false" label="report counts (-c)" help="Is ignored if k nearest neighbor search is enabled" />
             </when>
             <when value="obabel">
                 <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/>
@@ -95,87 +97,20 @@
 
 **What it does**
 
-similarity search of fingerprint data sets
+Similarity search of compounds using fingerprint data sets. Depending on the input either chemfp_ of `Open Babel`_ is used.
 
------
 
-**Example**
+**References**
 
-* input::
-	
-	      - Target Database in FPS format
+Please reference the `Open Babel`_ or the chemfp_ project.
 
-			#FPS1
-			#num_bits=881
-			#type=CACTVS-E_SCREEN/1.0 extended=2
-			#software=CACTVS/unknown
-			#source=Desktop/3579363516810334491.sdf
-			#date=2012-02-03T13:07:47
-			07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960
-			cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2926101609401b13e408000000000001
-			00200000040080000010000002000000000000	55169009
-			07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960
-			cc0bed3248000580644626004101b4844805901b041c2e19111e45039b8b2926105609401313e408000000000001
-			00200000040080000010000002000000000000	55079807
-			07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e960
-			cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e408000000000001
-			00200000040080000010000002000000000000	3153534
-			07ce0c000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e960
-			cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2926101609401b13e408000000000001
-			00200000040080000010000002000000000000	55168823
-			07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960
-			cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e408000000000001
-			00200000040080000010000002000000000000	55102353
-			07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e9
-			60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800003000
-			000100200000040080000010000002000000000000	55091849
-			07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e9
-			60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
-			000100200000040080000010000002000000000000	55091752
-			07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e9
-			60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000
-			000100200000040080000010000002000000000000	55091467
-			07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
-			60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
-			000100200000040080000010000002000000000000	55091466
-			07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
-			60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
-			000100200000040080000010000002000000000000	55091416
-			03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
-			60cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
-			000100200000040080000010000002000000000000	6499094
-			03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
-			60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
-			000100200000040080000010000002000000000000	6485578
-			07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e9
-			60cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000
-			000100200000040080000010000002000000000000	6485577
+N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. `DOI:10.1186/1758-2946-3-33`_
+The Open Babel Package http://openbabel.sourceforge.net/
+
 
-		- query : 
-			#FPS1
-			#num_bits=881
-			#type=CACTVS-E_SCREEN/1.0 extended=2
-			#software=CACTVS/unknown
-			#source=CID_28434379.sdf
-			#date=2012-02-03T13:08:39
-			07ce04000000000000000000000000000080060000000c060000000000001a800f0000780008100000101487e9
-			608c0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
-			000100200000040080000010000002000000000000	28434379
-		- k : 4
-		- threshold : 0.7
-
-* output::
-
-	#Simsearch/1
-	#num_bits=881
-	#type=Tanimoto k=4 threshold=0.7
-	#software=chemfp/1.0
-	#queries=q.fps
-	#targets=target.fps
-	#query_sources=CID_28434379.sdf
-	#target_sources=Desktop/3579363516810334491.sdf
-	4	28434379	55091752	0.9684	55091466	0.9682	55091416	0.9682	55102353	0.9682
-
+.. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33
+.. _chemfp: http://chemfp.com/
+.. _`Open Babel`: http://openbabel.org/
 
     </help>
 </tool>
diff -r dbe9c82028d1 -r 47d2bf691908 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Jun 01 20:03:57 2013 +0200
+++ b/tool_dependencies.xml	Sun Jun 02 19:54:51 2013 +0200
@@ -4,6 +4,6 @@
         <repository changeset_revision="3a993ff17df5" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="chemfp" version="1.1p1">
-        <repository changeset_revision="3e3356b13281" name="package_chemfp_1_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="616ee8e4abf4" name="package_chemfp_1_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
 </tool_dependency>
\ No newline at end of file