Mercurial > repos > bgruening > openbabel
diff filter/ob_grep.xml @ 0:527ecd2fc500 draft
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author | bgruening |
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date | Thu, 15 Aug 2013 03:25:06 -0400 |
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children | 125da3a296ca |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter/ob_grep.xml Thu Aug 15 03:25:06 2013 -0400 @@ -0,0 +1,98 @@ +<tool id="ctb_obgrep" name="Compound Search" version="0.1"> + <description>an advanced molecular grep program using SMARTS</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="2.3.2">openbabel</requirement> + </requirements> + <command> + ## The command is a Cheetah template which allows some Python based syntax. + ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces + obgrep + + $invert_matches + #if $n_times != 0: + -t $n_times + #end if + + $only_name + $full_match + $number_of_matches + -i ${infile.ext} + "${smarts_pattern}" + "${infile}" + > "${outfile}" 2>&1 + </command> + <inputs> + <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format."/> + <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/> + <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" falsevalue="" checked="false" /> + <param name="n_times" type="integer" value="0" label="Print a molecule only if the pattern occurs # times inside the molecule" /> + <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" /> + <param name="full_match" type="boolean" label="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern" truevalue="-f" falsevalue="" checked="false" /> + <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" /> + </inputs> + <options sanitize="False"/> + <outputs> + <data name="outfile" format_source="infile" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="infile" ftype="smi" value="8_mol.smi"/> + <param name="smarts_pattern" value="CO"/> + <param name="invert_matches" value="" /> + <param name="n_times" value="0"/> + <param name="only_name" value="" /> + <param name="full_match" value="" /> + <param name="number_of_matches" value="" /> + <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/> + </test> + </tests> + <help> + +.. class:: infomark + +**What this tool does** + +Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files. +It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_. + + +.. _Obgrep: http://openbabel.org/wiki/Obgrep +.. _here: http://openbabel.org/wiki/SMARTS + +----- + +.. class:: infomark + +**Input** + +| - `SD-Format`_ +| - `SMILES Format`_ + +.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification + +----- + +.. class:: infomark + +**Output** + +Same as input format. + +----- + +.. class:: infomark + +**Cite** + +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 + +`Open Babel`_ + +.. _`Open Babel`: http://openbabel.org/wiki/Main_Page + + </help> +</tool>