| Previous changeset 3:892811a1f12c (2017-05-20) Next changeset 5:57a1a58056a6 (2017-05-20) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807 |
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modified:
simsearch.xml |
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| diff -r 892811a1f12c -r 685a138131f0 simsearch.xml --- a/simsearch.xml Sat May 20 08:41:21 2017 -0400 +++ b/simsearch.xml Sat May 20 12:45:01 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<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> @@ -6,9 +6,10 @@ <command> <![CDATA[ #if $method_opts.method_opts_selector == "chemfp": - ln -s "${method_opts.query_opts.targets}" ./targets.fps && + 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 && + ln -s '${method_opts.query_opts.query}' ./query.fps && #end if simsearch @@ -35,23 +36,23 @@ ./targets.fps && - mv ./output.fps "${outfile}" + 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 $temp_link + ln -s '$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> @@ -110,22 +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> |