changeset 5:57a1a58056a6 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit d786052cd04f8b25eb4aff80b1b9724f62031b61
author bgruening
date Sat, 20 May 2017 12:57:06 -0400
parents 685a138131f0
children e3a7d6cc87af
files butina_clustering.py butina_clustering.xml mol2fps.xml nxn_clustering.py nxn_clustering.xml sdf2fps.xml simsearch.xml static/images/NxN_clustering.png static/images/NxN_clustering.svg test-data/CID_2244.can test-data/CID_2244.inchi test-data/CID_2244.sdf test-data/CID_2244.smi test-data/CID_2244_FP2.fps test-data/CID_2244_FP3.fps test-data/CID_2244_FP4.fps test-data/CID_2244_MACCS.fps test-data/CID_2244_maccs.fps test-data/NxN_Clustering_on_q.svg test-data/Taylor-Butina_Clustering_on_data_q.txt test-data/sdf2fps_result1.fps test-data/simsearch_on_tragets_and_q.tabular
diffstat 22 files changed, 4004 insertions(+), 130 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/butina_clustering.py	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+"""
+    Modified version of code examples from the chemfp project.
+    http://code.google.com/p/chem-fingerprints/
+    Thanks to Andrew Dalke of Andrew Dalke Scientific!
+"""
+
+import chemfp
+import sys
+import os
+import tempfile
+import argparse
+import subprocess
+from chemfp import search
+
+def unix_sort(results):
+    temp_unsorted = tempfile.NamedTemporaryFile(delete=False)
+    for (i,indices) in enumerate( results.iter_indices() ):
+        temp_unsorted.write('%s %s\n' % (len(indices), i))
+    temp_unsorted.close()
+    temp_sorted = tempfile.NamedTemporaryFile(delete=False)
+    temp_sorted.close()
+    p = subprocess.Popen(['sort', '-n', '-r', '-k', '1,1'], stdin=open(temp_unsorted.name), stdout=open(temp_sorted.name, 'w+'))
+    stdout, stderr = p.communicate()
+    return_code = p.returncode
+
+    if return_code:
+        sys.stdout.write(stdout)
+        sys.stderr.write(stderr)
+        sys.stderr.write("Return error code %i from command:\n" % return_code)
+    temp_sorted.close()
+    os.remove(temp_unsorted.name)
+
+    for line in open(temp_sorted.name):
+        size, fp_idx = line.strip().split()
+        yield (int(size), int(fp_idx))
+
+    os.remove(temp_sorted.name)
+
+def butina( args ):
+    """
+        Taylor-Butina clustering from the chemfp help.
+    """
+    out = args.output_path
+    targets = chemfp.open( args.input_path, format='fps' )
+    arena = chemfp.load_fingerprints( targets )
+
+    chemfp.set_num_threads( args.processors )
+    results = search.threshold_tanimoto_search_symmetric(arena, threshold = args.tanimoto_threshold)
+    results.reorder_all("move-closest-first")
+
+    sorted_ids = unix_sort(results)
+
+    # Determine the true/false singletons and the clusters
+    true_singletons = []
+    false_singletons = []
+    clusters = []
+
+    seen = set()
+    #for (size, fp_idx, members) in results:
+    for (size, fp_idx) in sorted_ids:
+        members = results[fp_idx].get_indices()
+        #print arena.ids[ fp_idx ], [arena.ids[ m ] for m in members]
+        if fp_idx in seen:
+            # Can't use a centroid which is already assigned
+            continue
+        seen.add(fp_idx)
+
+        if size == 0:
+            # The only fingerprint in the exclusion sphere is itself
+            true_singletons.append( fp_idx )
+            continue
+
+        # Figure out which ones haven't yet been assigned
+        unassigned = set(members) - seen
+
+        if not unassigned:
+            false_singletons.append(fp_idx)
+            continue
+
+        # this is a new cluster
+        clusters.append( (fp_idx, unassigned) )
+        seen.update(unassigned)
+
+    len_cluster = len(clusters)
+    #out.write( "#%s true singletons: %s\n" % ( len(true_singletons), " ".join(sorted(arena.ids[idx] for idx in true_singletons)) ) )
+    #out.write( "#%s false singletons: %s\n" % ( len(false_singletons), " ".join(sorted(arena.ids[idx] for idx in false_singletons)) ) )
+
+    out.write( "#%s true singletons\n" % len(true_singletons) )
+    out.write( "#%s false singletons\n" % len(false_singletons) )
+    out.write( "#clusters: %s\n" % len_cluster )
+
+    # Sort so the cluster with the most compounds comes first,
+    # then by alphabetically smallest id
+    def cluster_sort_key(cluster):
+        centroid_idx, members = cluster
+        return -len(members), arena.ids[centroid_idx]
+
+    clusters.sort(key=cluster_sort_key)
+
+    for centroid_idx, members in clusters:
+        centroid_name = arena.ids[centroid_idx]
+        out.write("%s\t%s\t%s\n" % (centroid_name, len(members), " ".join(arena.ids[idx] for idx in members)))
+        #ToDo: len(members) need to be some biggest top 90% or something ...
+
+    for idx in true_singletons:
+        out.write("%s\t%s\n" % (arena.ids[idx], 0))
+
+    out.close()
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="""Taylor-Butina clustering for fps files.
+For more details please see the original publication or the chemfp documentation:
+http://www.chemomine.co.uk/dbclus-paper.pdf
+https://chemfp.readthedocs.org
+""")
+
+    parser.add_argument("-i", "--input", dest="input_path",
+                    required=True,
+                    help="Path to the input file.")
+
+    parser.add_argument("-o", "--output", dest="output_path", type=argparse.FileType('w'),
+                    default=sys.stdout,
+                    help="Path to the output file.")
+
+    parser.add_argument("-t", "--threshold", dest="tanimoto_threshold", type=float,
+                    default=0.8,
+                    help="Tanimoto threshold [0.8]")
+
+    parser.add_argument('-p', '--processors', type=int, default=4)
+
+    options = parser.parse_args()
+    butina( options )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/butina_clustering.xml	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,93 @@
+<tool id="ctb_chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.2">
+    <description>of molecular fingerprints</description>
+    <requirements>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+        <requirement type="package" version="2.4.1">openbabel</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+<![CDATA[
+        python '$__tool_directory__/butina_clustering.py'
+            -i '$infile'
+            -t $threshold
+            -o '$outfile'
+            -p \${GALAXY_SLOTS:-1}
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
+        <param name='threshold' type='float' value='0.8'/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="fps" value="targets.fps"/>
+            <param name='threshold' value='0.8' ></param>
+            <output name="outfile" ftype="tabular"  file='Taylor-Butina_Clustering_on_data_q.txt'/>
+        </test>
+    </tests>
+<help>
+<![CDATA[
+
+
+.. class:: infomark
+
+**What this tool does**
+
+Unsupervised non-hierarchical clustering method based on the Taylor-Butina algorithm, which guarantees that every cluster contains molecules which are within a distance cutoff of the central molecule. This tool is based on the chemfp_ project.
+
+.. _chemfp: http://chemfp.com/
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+| Molecular fingerprints in FPS format.
+| Open Babel Fastsearch index is not supported.
+
+* Example::
+
+	-  fingerprints in FPS format
+
+		#FPS1
+		#num_bits=881
+		#type=CACTVS-E_SCREEN/1.0 extended=2
+		#software=CACTVS/unknown
+		#source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat
+		#date=2012-02-09T13:20:37
+		07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e
+		19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000	55169009
+		07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e
+		19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000	55079807
+		........
+
+	- Tanimoto threshold : 0.8 (between 0 and 1)
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+* Example::
+
+	0 true singletons
+	=>
+
+	0 false singletons
+	=>
+
+	1 clusters
+	55091849 has 12 other members
+	=> 6499094 6485578 55079807 3153534 55102353 55091466 55091416 6485577 55169009 55091752 55091467 55168823
+
+
+]]>
+ </help>
+    <citations>
+        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mol2fps.xml	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,276 @@
+<tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.3.0">
+    <description>with different fingerprint types</description>
+    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism-->
+    <requirements>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+        <requirement type="package" version="2016.03.3">rdkit</requirement>
+        <requirement type="package" version="2.4.1">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        #set $fptype = $fp_opts.fp_opts_selector
+
+        #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
+            ## Open Babel fingerprints
+            ob2fps $fptype --in '${infile.ext}' '${infile}' -o '${outfile}'
+        #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
+            #end if
+        #end if
+        --errors report 2>&1
+]]>
+    </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" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" 
+                    label="include information about the number of hydrogens on each atom" />
+            </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" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false"
+                    label="include information about the number of hydrogens on each atom" />
+                <param name="useChirality" type="boolean" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false"
+                    label="include information about the number of hydrogens on each atom" />
+                <param name="useBondTypes" type="boolean" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true"
+                    label="include information about the number of hydrogens on each atom" />
+            </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="fp_opts.fp_opts_selector" value="--FP2" />
+            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fp_opts.fp_opts_selector" value="--FP2" />
+            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>
+        </test>
+        <!-- FP3 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fp_opts.fp_opts_selector" value="--FP3" />
+            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fp_opts.fp_opts_selector" value="--FP3" />
+            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>
+        </test>
+        <!-- FP4 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fp_opts.fp_opts_selector" value="--FP4" />
+            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fp_opts.fp_opts_selector" value="--FP4" />
+            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>
+        </test>
+        <!-- MACCS -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fp_opts.fp_opts_selector" value="--MACCS" />
+            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fp_opts.fp_opts_selector" value="--MACCS" />
+            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+This tool uses chemfp_ to calculate 10 different fingerprints of common file formats. Chemfp uses `Open Babel`_, OpenEye_ and RDKit_.
+
+For more information check the websites listed below::
+
+	- http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity
+	- http://openbabel.org/wiki/Tutorial:Fingerprints
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+FPS fingerprint file format
+
+* Example::
+
+	      - 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
+		  ......
+
+			>PUBCHEM_COMPOUND_CID<
+			28434379
+
+			> <PUBCHEM_COMPOUND_CANONICALIZED>
+			1
+
+			> <PUBCHEM_CACTVS_COMPLEXITY>
+			280
+
+			> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
+			2
+
+			> <PUBCHEM_CACTVS_HBOND_DONOR>
+			2
+
+			> <PUBCHEM_CACTVS_ROTATABLE_BOND>
+			2
+
+			> <PUBCHEM_CACTVS_SUBSKEYS>
+			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
+
+			>
+
+		- type : FP2
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+* Example::
+
+	#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>
+    <citations>
+        <citation type="doi">10.1186/1758-2946-3-33</citation>
+        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
+        <citation type="bibtex">
+            @electronic{rdkit,
+                title = {RDKit: Open-source cheminformatics},
+                url ={http://www.rdkit.org}
+            }
+        </citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nxn_clustering.py	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+"""
+    Modified version of code examples from the chemfp project.
+    http://code.google.com/p/chem-fingerprints/
+    Thanks to Andrew Dalke of Andrew Dalke Scientific!
+"""
+import matplotlib
+matplotlib.use('Agg')
+import argparse
+import os
+import chemfp
+import scipy.cluster.hierarchy as hcluster
+import pylab
+import numpy
+
+def distance_matrix(arena, tanimoto_threshold = 0.0):
+    n = len(arena)
+    # Start off a similarity matrix with 1.0s along the diagonal
+    try:
+        similarities = numpy.identity(n, "d")
+    except:
+        raise Exception('Input dataset is to large!')
+    chemfp.set_num_threads( args.processors )
+
+    ## Compute the full similarity matrix.
+    # The implementation computes the upper-triangle then copies
+    # the upper-triangle into lower-triangle. It does not include
+    # terms for the diagonal.
+    results = chemfp.search.threshold_tanimoto_search_symmetric(arena, threshold=tanimoto_threshold)
+
+    # Copy the results into the NumPy array.
+    for row_index, row in enumerate(results.iter_indices_and_scores()):
+        for target_index, target_score in row:
+            similarities[row_index, target_index] = target_score
+
+    # Return the distance matrix using the similarity matrix
+    return 1.0 - similarities
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="""NxN clustering for fps files.
+For more details please see the chemfp documentation:
+https://chemfp.readthedocs.org
+""")
+
+    parser.add_argument("-i", "--input", dest="input_path",
+                    required=True,
+                    help="Path to the input file.")
+
+    parser.add_argument("-c", "--cluster", dest="cluster_image",
+                    help="Path to the output cluster image.")
+
+    parser.add_argument("-s", "--smatrix", dest="similarity_matrix",
+                    help="Path to the similarity matrix output file.")
+
+    parser.add_argument("-t", "--threshold", dest="tanimoto_threshold", 
+                    type=float, default=0.0,
+                    help="Tanimoto threshold [0.0]")
+
+    parser.add_argument("--oformat", default='png', help="Output format (png, svg)")
+
+    parser.add_argument('-p', '--processors', type=int, 
+        default=4)
+
+    args = parser.parse_args()
+
+    targets = chemfp.open( args.input_path, format='fps' )
+    arena = chemfp.load_fingerprints( targets )
+    distances  = distance_matrix( arena, args.tanimoto_threshold )
+
+    if args.similarity_matrix:
+        distances.tofile( args.similarity_matrix )
+
+    if args.cluster_image:
+        linkage = hcluster.linkage( distances, method="single", metric="euclidean" )
+
+        hcluster.dendrogram(linkage, labels=arena.ids)
+
+        pylab.savefig( args.cluster_image, format=args.oformat )
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nxn_clustering.xml	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,120 @@
+<tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.4">
+    <description>of molecular fingerprints</description>
+    <requirements>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+        <requirement type="package" version="2">python</requirement>
+        <requirement type="package" version="2.0.2">matplotlib</requirement>
+        <requirement type="package" version="0.19.0">scipy</requirement>
+        <requirement type="package" version="2.4.1">openbabel</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+<![CDATA[
+        python '$__tool_directory__/nxn_clustering.py'
+            -i '$infile'
+            -t $threshold
+            #if str($output_files) in ['both', 'image']:
+                --cluster '$image'
+            #end if
+            #if str($output_files) in ['both', 'matrix']:
+                --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"/>
+        <param name='threshold' type='float' value='0.0' />
+        <param name='oformat' type='select' format='text' label="Format of the resulting picture">
+            <option value='png'>PNG</option>
+            <option value='svg'>SVG</option>
+        </param>
+        <param name='output_files' type='select' format='text' label="Output options">
+            <option value='both'>NxN matrix and Image</option>
+            <option value='image'>Image</option>
+            <option value='matrix'>NxN Matrix</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="image" format="svg" label="${tool.name} on ${on_string} - Cluster Image">
+            <filter>output_files == "both" or output_files == "image"</filter>
+            <change_format>
+                <when input="oformat" value="png" format="png"/>
+            </change_format>
+        </data>
+        <data name="smilarity_matrix" format="binary" label="${tool.name} on ${on_string} - Similarity Matrix">
+            <filter>output_files == "both" or output_files == "matrix"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="fps" value="targets.fps" />
+            <param name='treshold' value='0.75' />
+            <param name='oformat' value='svg' />
+            <param name='output_files' value='image' />
+            <output name="image" file='NxN_Clustering_on_q.svg' ftype="svg" compare="sim_size"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Generating hierarchical clusters and visualizing clusters with dendrograms.
+For the clustering and the fingerprint handling the chemfp_ project is used.
+
+.. _chemfp: http://chemfp.com/
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+The plotting of the cluster image is sensible only with a small dataset.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+Molecular fingerprints in FPS format. Open Babel Fastsearch index is not supported.
+
+* Example::
+
+	-  fingerprints in FPS format
+
+		#FPS1
+		#num_bits=881
+		#type=CACTVS-E_SCREEN/1.0 extended=2
+		#software=CACTVS/unknown
+		#source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat
+		#date=2012-02-09T13:20:37
+		07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e
+		19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000	55169009
+		07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e
+		19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000	55079807
+		........
+
+	- Tanimoto threshold : 0.8 (between 0 and 1)
+
+-----
+
+.. class:: informark
+
+**Output**
+
+* Example::
+
+	.. image:: $PATH_TO_IMAGES/NxN_clustering.png
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sdf2fps.xml	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,116 @@
+<tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="0.2">
+    <description>extract fingerprints from sdf files metadata</description>
+    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
+    <requirements>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+        <requirement type="package" version="2.4.1">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        sdf2fps --pubchem '${infile}' > '${outfile}'
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fps"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="sdf" value="CID_2244.sdf" />
+            <output name="outfile" file='sdf2fps_result1.fps' ftype="fps" lines_diff="4" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Read an input SD file, extract the fingerprints and store them in a FPS-file.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+`SD-Format`_
+
+.. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file
+
+* Example::
+
+		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
+		  ......
+
+			>PUBCHEM_COMPOUND_CID<
+			28434379
+
+			> <PUBCHEM_COMPOUND_CANONICALIZED>
+			1
+
+			> <PUBCHEM_CACTVS_COMPLEXITY>
+			280
+
+			> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
+			2
+
+			> <PUBCHEM_CACTVS_HBOND_DONOR>
+			2
+
+			> <PUBCHEM_CACTVS_ROTATABLE_BOND>
+			2
+
+			> <PUBCHEM_CACTVS_SUBSKEYS>
+			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
+
+			>
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+* Example::
+
+	#FPS1
+	#num_bits=881
+	#type=CACTVS-E_SCREEN/1.0 extended=2
+	#software=CACTVS/unknown
+	#source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat
+	#date=2012-02-03T10:44:12
+	07ce04000000000000000000000000000080060000000c0600
+	00000000001a800f0000780008100000101487e9608c0bed32
+	48000580644626204101b4844805901b041c2e19511e45039b
+	8b2924101609401b13e4080000000000010020000004008000
+	0010000002000000000000	28434379
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
+    </citations>
+</tool>
--- a/simsearch.xml	Sat May 20 12:45:01 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
-<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>
-    </requirements>
-    <command>
-<![CDATA[
-        #if $method_opts.method_opts_selector == "chemfp":
-            ln -s '${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
-                    $method_opts.counts
-                #else:
-                    #set $k = int($method_opts.knn)
-                #end if
-
-                -k $k
-                --threshold $method_opts.threshold
-                -o ./output.fps
-
-                ## build and search an in-memory data structure (faster for multiple queries)
-                --memory
-
-                #if $method_opts.query_opts.query_opts_selector == "normal":
-                    -q ./query.fps
-                #else:
-                    --NxN
-                #end if
-
-                ./targets.fps
-                &&
-                mv ./output.fps '${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.
-            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>
-              <option value="obabel">OpenBabel Fastsearch Index</option>
-            </param>
-            <when value="chemfp">
-                <conditional name="query_opts">
-                    <param name="query_opts_selector" type="select" label="Query Mode">
-                      <option value="normal">Query molecules are stores in a separate file</option>
-                      <option value="nxn">Target molecules are also queries (NxN)</option>
-                    </param>
-                    <when value="normal">
-                        <param name='query' type='data' format="fps" label='Query molecules'/>
-                        <param name='targets' type='data' format="fps" label='Target molecules'/>
-                    </when>
-                    <when value="nxn">
-                        <param name='targets' type='data' format="fps" label='Target moleculs'/>
-                    </when>
-                </conditional>
-                <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' 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"/>
-                <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
-                <param name="threshold" type='float' label="threshold" value='0.7'/>
-            </when>
-        </conditional>
-
-    </inputs>
-    <outputs>
-        <data name="outfile" format="tabular" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="targets" ftype="fps" value="targets.fps"/>
-            <param name="query" ftype="fps" value="q.fps"/>
-            <param name="k" value='4'/>
-            <param name="th" value='0.7'/>
-            <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
-        </test>
-    </tests>
-    <help>
-<![CDATA[
-
-
-.. class:: infomark
-
-**What this tool does**
-
-Similarity searches using a variety of different fingerprints using either the chemfp_ FPS type or the Open Babel FastSearch_ index.
-
-.. _chemfp: http://chemfp.com/
-.. _FastSearch: http://openbabel.org/wiki/FastSearch
-
-
-]]>
-    </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>
Binary file static/images/NxN_clustering.png has changed
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+++ b/static/images/NxN_clustering.svg	Sat May 20 12:57:06 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CID_2244.inchi	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,1 @@
+InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CID_2244.sdf	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,154 @@
+2244
+  -OEChem-05151212332D
+
+ 21 21  0     0  0  0  0  0  0999 V2000
+    3.7320   -0.0600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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+
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+1
+
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+
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+1
+
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+3
+
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+
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+2-acetoxybenzoic acid
+
+> <PUBCHEM_IUPAC_CAS_NAME>
+2-acetyloxybenzoic acid
+
+> <PUBCHEM_IUPAC_NAME>
+2-acetyloxybenzoic acid
+
+> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
+2-acetyloxybenzoic acid
+
+> <PUBCHEM_IUPAC_TRADITIONAL_NAME>
+2-acetoxybenzoic acid
+
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+
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+BSYNRYMUTXBXSQ-UHFFFAOYSA-N
+
+> <PUBCHEM_XLOGP3>
+1.2
+
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+
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+C9H8O4
+
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+180.15742
+
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+CC(=O)OC1=CC=CC=C1C(=O)O
+
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+CC(=O)OC1=CC=CC=C1C(=O)O
+
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+63.6
+
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+180.042259
+
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+0
+
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+13
+
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+0
+
+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
+0
+
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+0
+
+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
+0
+
+> <PUBCHEM_COMPONENT_COUNT>
+1
+
+> <PUBCHEM_CACTVS_TAUTO_COUNT>
+1
+
+> <PUBCHEM_COORDINATE_TYPE>
+1
+5
+255
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+5  6  8
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+
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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@@ -0,0 +1,7 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CID_2244_FP3.fps	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,7 @@
+#FPS1
+#num_bits=1021
+#type=OpenBabel-FP2/1
+#software=OpenBabel/2.4.1
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CID_2244_FP4.fps	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,7 @@
+#FPS1
+#num_bits=1021
+#type=OpenBabel-FP2/1
+#software=OpenBabel/2.4.1
+#source=/tmp/tmptaAke4/files/000/dataset_11.dat
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CID_2244_MACCS.fps	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,7 @@
+#FPS1
+#num_bits=1021
+#type=OpenBabel-FP2/1
+#software=OpenBabel/2.4.1
+#source=/tmp/tmptaAke4/files/000/dataset_15.dat
+#date=2017-05-19T13:55:30
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CID_2244_maccs.fps	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,7 @@
+#FPS1
+#num_bits=166
+#type=OpenBabel-MACCS/2
+#software=OpenBabel/2.3.1
+#source=CID_2244.sdf
+#date=2012-05-15T17:00:39
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Taylor-Butina_Clustering_on_data_q.txt	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,4 @@
+#0 true singletons
+#0 false singletons
+#clusters: 1
+55091752	12	6499094 6485578 55079807 3153534 55102353 55091466 55091416 6485577 55169009 55091467 55168823 55091849
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sdf2fps_result1.fps	Sat May 20 12:57:06 2017 -0400
@@ -0,0 +1,7 @@
+#FPS1
+#num_bits=881
+#type=CACTVS-E_SCREEN/1.0 extended=2
+#software=CACTVS/unknown
+#source=/tmp/tmpN2w37z/files/000/dataset_1.dat
+#date=2017-05-19T14:27:41
+030e1c000000000000000000000000000000000000000c00000000000000008000000058000010000030200119004c70010060001140044b100040100024040010118060101330e46c21ac5841de06a50788109de11113047100000000001000000000000000080000000000000000	2244
--- a/test-data/simsearch_on_tragets_and_q.tabular	Sat May 20 12:45:01 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-#Simsearch/1
-#num_bits=881
-#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
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