comparison simsearch.xml @ 4:685a138131f0 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807

3:892811a1f12c

<tool id="ctb_simsearch" name="Similarity Search" version="0.1.1">
    <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'

                    --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.
            #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($method_opts.fastsearch.files_path,'molecule.fs')}" -S "${temp_link}" -at${method_opts.threshold} -O "${outfile}" -osmi -aa 2>&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>

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

-----

.. 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>
    </citations>
</tool>

4:685a138131f0

<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'

                    --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>

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>