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changeset 16:987b62da416d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61
author bgruening
date Sat, 20 May 2017 13:05:53 -0400
parents b4eaf75cac77
children e1e2746c8688
files force_pre-commit_hook_temp_file simsearch.xml test-data/simsearch_on_tragets_and_q.tabular test-data/target.fps test-data/targets.fps tool_dependencies.xml
diffstat 5 files changed, 54 insertions(+), 63 deletions(-) [+]
line wrap: on
line diff
--- a/simsearch.xml	Fri Jul 19 16:28:47 2013 +0200
+++ b/simsearch.xml	Sat May 20 13:05:53 2017 -0400
@@ -1,12 +1,18 @@
-<tool id="ctb_simsearch" name="Similarity Search" version="0.1.1">
+<tool id="ctb_simsearch" name="Similarity Search" version="0.2">
     <description>of fingerprint data sets</description>
     <requirements>
         <requirement type="package" version="1.1p1">chemfp</requirement>
-        <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command>
+<![CDATA[
         #if $method_opts.method_opts_selector == "chemfp":
-            simsearch 
+            ln -s '${method_opts.query_opts.targets}' ./targets.fps &&
+
+            #if $method_opts.query_opts.query_opts_selector == "normal":
+                ln -s '${method_opts.query_opts.query}' ./query.fps &&
+            #end if
+
+            simsearch
                 #if int($method_opts.knn) == 0:
                     #set $k = 'all'
                     ## count is only available if k nearest neighbor search is disabled
@@ -15,38 +21,38 @@
                     #set $k = int($method_opts.knn)
                 #end if
 
-                -k $k 
-
+                -k $k
                 --threshold $method_opts.threshold
-                --query-format fps
-                --target-format fps
-                -o "${outfile}"
+                -o ./output.fps
 
                 ## build and search an in-memory data structure (faster for multiple queries)
                 --memory
 
                 #if $method_opts.query_opts.query_opts_selector == "normal":
-                    -q "${method_opts.query_opts.query}"
+                    -q ./query.fps
                 #else:
                     --NxN
                 #end if
 
-                "${method_opts.query_opts.targets}" 
+                ./targets.fps
+                &&
+                mv ./output.fps '${outfile}'
         #else:
             ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
             ## Furthermore OpenBabel is really picky with file extensions. We need to specify every datatype. I did not find a solution to specify the query-filetype.
             ## A workaround is to create a symlink with a proper file-extension.
-            #import tempfile
-            #set $temp_file = tempfile.NamedTemporaryFile()
-            #set $temp_link = "%s.%s" % ($temp_file.name, $method_opts.query.ext)
-            $temp_file.close()
-            ln -s $method_opts.query $temp_link;
-            obabel -i fs "${os.path.join($method_opts.fastsearch.extra_files_path,'molecule.fs')}" -S "${temp_link}" -at${method_opts.threshold} -O "${outfile}" -osmi -aa 2>&#38;1;
-            rm $temp_link
+            ln -s '$method_opts.query' ./temp_query.$method_opts.query.ext
+            obabel 
+                -i fs '$method_opts.fastsearch.files_path/molecule.fs'
+                -S ./temp_query.$method_opts.query.ext
+                -at${method_opts.threshold}
+                -O '${outfile}'
+                -osmi
+                -aa
         #end if
+]]>
     </command>
     <inputs>
-
         <conditional name="method_opts">
             <param name="method_opts_selector" type="select" label="Subject database/sequences">
               <option value="chemfp">Chemfp fingerprint file</option>
@@ -93,6 +99,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 
 
 .. class:: infomark
@@ -104,18 +111,11 @@
 .. _chemfp: http://chemfp.com/
 .. _FastSearch: http://openbabel.org/wiki/FastSearch
 
------
 
-.. class:: infomark
-
-**Cite**
-
-| The 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
-
-
+]]>
     </help>
+    <citations>
+        <citation type="doi">10.1186/1758-2946-3-33</citation>
+        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
+    </citations>
 </tool>
--- a/test-data/simsearch_on_tragets_and_q.tabular	Fri Jul 19 16:28:47 2013 +0200
+++ b/test-data/simsearch_on_tragets_and_q.tabular	Sat May 20 13:05:53 2017 -0400
@@ -1,9 +1,9 @@
 #Simsearch/1
 #num_bits=881
-#type=Tanimoto k=4 threshold=0.7
-#software=chemfp/1.0
-#queries=q.fps
-#targets=target.fps
+#type=Tanimoto k=all threshold=0.7
+#software=chemfp/1.1p1
+#queries=./query.fps
+#targets=./targets.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
+13	28434379	6499094	0.9615	6485578	0.9679	55079807	0.9313	3153534	0.9557	55102353	0.9682	55091466	0.9682	55091416	0.9682	6485577	0.9497	55169009	0.9560	55091752	0.9684	55091467	0.9623	55168823	0.9563	55091849	0.9563
--- a/test-data/target.fps	Fri Jul 19 16:28:47 2013 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-#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
-07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000	55169009
-07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000	55079807
-07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e960cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	3153534
-07ce0c000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000	55168823
-07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	55102353
-07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800003000000100200000040080000010000002000000000000	55091849
-07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	55091752
-07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000000100200000040080000010000002000000000000	55091467
-07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	55091466
-07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	55091416
-03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	6499094
-03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	6485578
-07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e960cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000000100200000040080000010000002000000000000	6485577
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/targets.fps	Sat May 20 13:05:53 2017 -0400
@@ -0,0 +1,19 @@
+#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
+07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000	55169009
+07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000	55079807
+07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e960cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	3153534
+07ce0c000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000	55168823
+07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	55102353
+07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800003000000100200000040080000010000002000000000000	55091849
+07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	55091752
+07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000000100200000040080000010000002000000000000	55091467
+07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	55091466
+07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	55091416
+03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	6499094
+03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	6485578
+07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e960cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000000100200000040080000010000002000000000000	6485577
--- a/tool_dependencies.xml	Fri Jul 19 16:28:47 2013 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool_dependency>
-    <package name="openbabel" version="2.3.2">
-        <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="616ee8e4abf4" name="package_chemfp_1_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    </package>
-</tool_dependency>
\ No newline at end of file