Mercurial > repos > luis > ball
diff galaxy_stubs/FingerprintSimilaritySearch.xml @ 2:605370bc1def draft default tip
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| author | luis |
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| date | Tue, 12 Jul 2016 12:33:33 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/FingerprintSimilaritySearch.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,114 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Chemoinformatics]--> +<tool id="FingerprintSimilaritySearch" name="FingerprintSimilaritySearch" version="1.1.0"> + <description>calculate similar molecules in a library</description> + <macros> + <token name="@EXECUTABLE@">FingerprintSimilaritySearch</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>FingerprintSimilaritySearch + +#if $param_t: + -t $param_t +#end if +#if $param_q: + -q $param_q +#end if +#if $param_o: + -o $param_o +#end if +#if $param_f: + -f $param_f +#end if +#if $param_fp_col: + -fp_col $param_fp_col +#end if +#if $param_id_col: + -id_col $param_id_col +#end if +#if $param_fp_tag: + -fp_tag "$param_fp_tag" +#end if +#if $param_id_tag: + -id_tag "$param_id_tag" +#end if +#if $param_tc: + -tc $param_tc +#end if +#if $param_nt: + -nt "$param_nt" +#end if +#if $param_bs: + -bs $param_bs +#end if +#if $param_sdf_out: + -sdf_out $param_sdf_out +#end if +</command> + <inputs> + <param name="param_t" type="data" format="smi.gz,csv,sdf.gz,sdf,txt.gz,smi,txt,csv.gz" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="Target library input file" help="(-t) "/> + <param name="param_q" type="data" format="smi.gz,csv,sdf.gz,sdf,txt.gz,smi,txt,csv.gz" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="Query library input file" help="(-q) "/> + <param name="param_f" type="integer" min="1" max="2" optional="False" value="0" label="Fingerprint format [1 = binary bitstring, 2 = comma separated feature list]" help="(-f) "/> + <param name="param_fp_col" type="integer" value="-1" label="Column number for comma separated smiles input which contains the fingerprint" help="(-fp_col) "/> + <param name="param_id_col" type="integer" value="-1" label="Column number for comma separated smiles input which contains the molecule identifie" help="(-id_col) "/> + <param name="param_fp_tag" type="text" size="30" value=" " label="Tag name for SDF input which contains the fingerprint" help="(-fp_tag) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_id_tag" type="text" size="30" value=" " label="Tag name for SDF input which contains the molecule identifie" help="(-id_tag) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_tc" type="float" value="0.7" label="Tanimoto cutoff [default: 0.7]" help="(-tc) "/> + <param name="param_nt" type="text" size="30" value="1" label="Number of parallel threads to use" help="(-nt) To use all possible threads enter <max> [default: 1]"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_bs" type="integer" value="500" label="Block size [default: 500]" help="(-bs) "/> + <param name="param_sdf_out" type="integer" min="0" max="1" optional="True" value="0" label="If query file has SD format, this flag activates writing of nearest neighbours as a new CSV tag in a copy of the query SD file" help="(-sdf_out) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_t" format="input"/> + </outputs> + <help>This tool calculates all nearest neighbours above a similarity cutoff for given query molecules in a compound library on the basis of 2D binary fingerprints. +The first library to specify (i1) is the compound library to be searched, the second library (i2) is conseiderd as the query compounds. +Both files have to be comma separated values (csv) files and the binary fingerprints have to be encoded as feature lists or as binary bit strings. + +WARNING: If similarity cutoff is chosen to be 0.0, the output will be the entire similarity matrix and has a size of n*m with n=|i1| and m=|i2|. + +====================================================================================================================================================== + +Examples: + +$ FingerprintSimilaritySearch -t target.sdf -q query.sdf -o results -fp_tag FPRINT -f 1 -id_tag NAME + tries to extract fingerprints as binary bitstrings (-f 1) from tag <FPRINT> and compound IDs from tag <NAME> of target.sdf and query.sdf. + A similarity search is performed for all query molecules against all target molecules and pairs with similarity above Tanimoto cutoff 0.7 are written to outfile (results). + +$ FingerprintSimilaritySearch -t target.sdf -q query.sdf -o results -fp_tag FPRINT -f 1 -id_tag NAME -sdf_out + tries to extract fingerprints as binary bitstrings (-f 1) from tag <FPRINT> and compound IDs from tag <NAME> of target.sdf and query.sdf. + A similarity search is performed for all query molecules against all target molecules and pairs with similarity above Tanimoto cutoff 0.7 + are added as a new SD tag to output file 'NN_TAGGED_query.sdf' as a list of TargetID:Similarity pairs. + +$ FingerprintSimilaritySearch -t target.sdf -q query.smi -o results -fp_tag FPRINT -f 1 -id_tag NAME -fp_col 2 + tries to extract fingerprints as binary bitstrings (-f 1) from tag <FPRINT> and compound IDs from tag <NAME> of target.sdf + and fingerprints as binary bitstrings of space separated query file from column 2 (-fp_col 2). + A similarity search is performed for all query molecules against all target molecules and pairs with similarity above Tanimoto cutoff 0.7 are written to outfile (results). + +</help> +</tool>