view simsearch.xml @ 2:b216c5c94dd1

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<tool id="chemfp_simsearch" name="Similarity Search" version="0.1">
    <description>of fingerprint data sets</description>
    <!--<parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="10000" shared_inputs="targets,fastsearch" merge_outputs="outfile"></parallelism>-->
    <requirements>
        <requirement type="package" version="1.1p1">chemfp</requirement>
    </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
            simsearch -k $method_opts.k --threshold $method_opts.threshold --in fps --target-format fps -q "${method_opts.query}" "${method_opts.targets}" -o "${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 fileextensions. 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
        #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">
                <param name="query" type='data' format="fps" label="query"/>
                <param name="targets" type='data' format="fps" label="Target database"/>
                <param name="k" type='text'  label="k nearest neighbor" value='all'/>
                <param name="threshold" type='float' label="threshold" value='0.7'/>
            </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>


**What it does**

similarity search of fingerprint data sets

-----

**Example**

* input::
	
	      - Target Database in FPS format

			#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

		- 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


    </help>
</tool>