Mercurial > repos > bgruening > chemfp
diff mol2fps.xml @ 38:02e03ac072cf draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
| author | bgruening |
|---|---|
| date | Tue, 07 May 2019 13:19:01 -0400 |
| parents | 73b8c87779ae |
| children | 0a1c281e9224 |
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--- a/mol2fps.xml Fri Mar 23 03:26:12 2018 -0400 +++ b/mol2fps.xml Tue May 07 13:19:01 2019 -0400 @@ -1,21 +1,20 @@ -<tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.3.0"> - <description>with different fingerprint types</description> +<tool id="ctb_chemfp_mol2fps" name="Molecule to fingerprint" version="1.5"> + <description>conversion to several different fingerprint formats</description> <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism--> <requirements> - <requirement type="package" version="1.1p1">chemfp</requirement> - <requirement type="package" version="2016.03.3">rdkit</requirement> + <requirement type="package" version="1.5">chemfp</requirement> + <requirement type="package" version="2018.09.3">rdkit</requirement> <requirement type="package" version="2.4.1">openbabel</requirement> </requirements> <command> <![CDATA[ - #set $fptype = $fp_opts.fp_opts_selector - #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']: + #if $fp_opts.fp_opts_selector in ['--FP2', '--FP3', '--FP4', '--MACCS']: ## Open Babel fingerprints - ob2fps $fptype --in '${infile.ext}' '${infile}' -o '${outfile}' + ob2fps $fp_opts.fp_opts_selector --in '${infile.ext}' '${infile}' -o '${outfile}' --out 'fps' #else: ## RDKit fingerprints - rdkit2fps --in '${infile.ext}' '${infile}' -o '${outfile}' + rdkit2fps --in '${infile.ext}' '${infile}' -o '${outfile}' --out 'fps' #if $fp_opts.fp_opts_selector == "--RDK": --RDK --fpSize $fp_opts.fpSize @@ -35,7 +34,7 @@ $fp_opts.useChirality $fp_opts.useBondTypes #elif $fp_opts.fp_opts_selector == "--pairs": - --paris + --pairs --fpSize $fp_opts.fpSize --minLength $fp_opts.minLength --maxLength $fp_opts.maxLength @@ -49,7 +48,7 @@ ]]> </command> <inputs> - <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/> + <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="Molecule file"/> <conditional name="fp_opts"> <param name="fp_opts_selector" type="select" label="Type of fingerprint"> <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option> @@ -68,51 +67,51 @@ <when value="--FP4" /> <when value="--MACCS" /> <when value="--RDK"> - <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> + <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help=""> <validator type="in_range" min="1" /> </param> - <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help=""> + <param name="minPath" type="integer" value="1" label="Minimum number of bonds to include in the subgraph" help=""> <validator type="in_range" min="1" /> </param> - <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help=""> + <param name="maxPath" type="integer" value="7" label="Maximum number of bonds to include in the subgraph" help=""> <validator type="in_range" min="1" /> </param> - <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help=""> + <param name="nBitsPerHash" type="integer" value="4" label="Number of bits to set per path" help=""> <validator type="in_range" min="1" /> </param> <param name="useHs" type="boolean" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" - label="include information about the number of hydrogens on each atom" /> + label="Include information about the number of hydrogens on each atom" /> </when> <when value="--torsions"> - <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> + <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help=""> <validator type="in_range" min="1" /> </param> - <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help=""> + <param name="targetSize" type="integer" value="4" label="Number of target bits in the fingerprint" help=""> <validator type="in_range" min="1" /> </param> </when> <when value="--morgan"> - <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> + <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help=""> <validator type="in_range" min="1" /> </param> - <param name="radius" type="integer" value="2" label="radius for the Morgan algorithm" help=""> + <param name="radius" type="integer" value="2" label="Radius for the Morgan algorithm" help=""> <validator type="in_range" min="1" /> </param> <param name="useFeatures" type="boolean" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false" - label="include information about the number of hydrogens on each atom" /> + label="Include information about the number of hydrogens on each atom" /> <param name="useChirality" type="boolean" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false" - label="include information about the number of hydrogens on each atom" /> + label="Include information about the number of hydrogens on each atom" /> <param name="useBondTypes" type="boolean" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true" - label="include information about the number of hydrogens on each atom" /> + label="Include information about the number of hydrogens on each atom" /> </when> <when value="--pairs"> - <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> + <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help=""> <validator type="in_range" min="1" /> </param> - <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help=""> + <param name="minLength" type="integer" value="1" label="Minimum bond count for a pair" help=""> <validator type="in_range" min="1" /> </param> - <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help=""> + <param name="maxLength" type="integer" value="30" label="Maximum bond count for a pair" help=""> <validator type="in_range" min="1" /> </param> </when> @@ -128,47 +127,73 @@ <!-- FP2 --> <test> <param name="infile" value="CID_2244.sdf" ftype="sdf" /> - <param name="fp_opts.fp_opts_selector" value="--FP2" /> + <conditional name="fp_opts"> + <param name="fp_opts_selector" value="--FP2" /> + </conditional> <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/> </test> <test> <param name="infile" value="CID_2244.smi" ftype="smi" /> - <param name="fp_opts.fp_opts_selector" value="--FP2" /> + <conditional name="fp_opts"> + <param name="fp_opts_selector" value="--FP2" /> + </conditional> <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/> </test> <!-- FP3 --> <test> <param name="infile" value="CID_2244.sdf" ftype="sdf" /> - <param name="fp_opts.fp_opts_selector" value="--FP3" /> + <conditional name="fp_opts"> + <param name="fp_opts_selector" value="--FP3" /> + </conditional> <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/> </test> <test> <param name="infile" value="CID_2244.smi" ftype="smi" /> - <param name="fp_opts.fp_opts_selector" value="--FP3" /> + <conditional name="fp_opts"> + <param name="fp_opts_selector" value="--FP3" /> + </conditional> <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/> </test> <!-- FP4 --> <test> <param name="infile" value="CID_2244.sdf" ftype="sdf" /> - <param name="fp_opts.fp_opts_selector" value="--FP4" /> + <conditional name="fp_opts"> + <param name="fp_opts_selector" value="--FP4" /> + </conditional> <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/> </test> <test> <param name="infile" value="CID_2244.smi" ftype="smi" /> - <param name="fp_opts.fp_opts_selector" value="--FP4" /> + <conditional name="fp_opts"> + <param name="fp_opts_selector" value="--FP4" /> + </conditional> <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/> </test> <!-- MACCS --> <test> <param name="infile" value="CID_2244.sdf" ftype="sdf" /> - <param name="fp_opts.fp_opts_selector" value="--MACCS" /> + <conditional name="fp_opts"> + <param name="fp_opts_selector" value="--MACCS" /> + </conditional> <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/> </test> <test> <param name="infile" value="CID_2244.smi" ftype="smi" /> - <param name="fp_opts.fp_opts_selector" value="--MACCS" /> + <conditional name="fp_opts"> + <param name="fp_opts_selector" value="--MACCS" /> + </conditional> <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/> </test> + <!-- RDKit2fps --> + <test> + <param name="infile" value="CID_2244.smi" ftype="smi" /> + <conditional name="fp_opts"> + <param name="fp_opts_selector" value="--torsions" /> + </conditional> + <param name="fp_opts.fpSize" value="2048" /> + <param name="fp_opts.targetSize" value="4" /> + <output name="outfile" file="CID_2244_torsions.fps" ftype="fps" lines_diff="4"/> + </test> </tests> <help> <![CDATA[ @@ -177,7 +202,7 @@ **What this tool does** -This tool uses chemfp_ to calculate 10 different fingerprints of common file formats. Chemfp uses `Open Babel`_, OpenEye_ and RDKit_. +This tool uses chemfp to calculate molecular fingerprints, supporting a number of common file formats. Chemfp uses OpenBabel, OpenEye and RDKit. For more information check the websites listed below:: @@ -194,7 +219,7 @@ * Example:: - - SDF File + - SD-File 28434379 -OEChem-02031205132D