Mercurial > repos > bgruening > ctb_im_screen
diff screen.xml @ 0:2c11d1f9e00b draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
| author | bgruening |
|---|---|
| date | Tue, 21 Jul 2020 05:22:46 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/screen.xml Tue Jul 21 05:22:46 2020 -0400 @@ -0,0 +1,145 @@ +<tool id="ctb_im_screen" name="Screen" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>a compound against a library using RDKit</description> + <macros> + <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + screen + #if $comparator.comparator_opts == 'str': + --qsmiles '${comparator.input}' + #else: + --qmolfile ${comparator.input} + #end if + + -i '$infile' + -if sdf + #if $comparator.comparator_opts == 'mol' + --isMol + #end if + #if $fragment_opts + -f '$fragment_opts' + #end if + --simmin '$sim_min' + --simmax '$sim_max' + -d '$descriptor_opts' + -m '$metric_opts' + #if $hac_min != '' + --hacmin '$hac_min' + #end if + #if $hac_max != '' + --hacmax '$hac_max' + #end if + #if $mw_min != '' + --mwmin '$mw_min' + #end if + #if $mw_max != '' + --mwmax '$mw_max' + #end if + --meta + -o outp &>> $logfile && ## the script does not exit 0 + cat outp_metrics.txt &>> $logfile && + gzip -d outp.sdf.gz + ]]></command> + <inputs> + <conditional name="comparator"> + <param name='comparator_opts' type='select' label="Input type" help="Enter SMILES string or Mol file."> + <option value='file'>Mol/SDF file</option> + <option value='str'>SMILES string</option> + </param> + <when value='str'> + <param name="input" type="text" label="SMILES input" help="Enter SMILES for a compound."> + <validator type='length' min='5'/> + </param> + </when> + <when value='file'> + <param name="input" type="data" format="sdf,mol" label="Input" help="Input file in mol/sdf format"/> + </when> + </conditional> + <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF or JSON format, for comparison"/> + <param name="sim_min" type="float" label="Similarity lower cutoff" value="0.7" min="0" max="1" help="(1.0 means identical)"/> + <param name="sim_max" type="float" label="Similarity upper cutoff" value="1.0" min="0" max="1" help="(1.0 means identical)"/> + <param name="descriptor_opts" type="select" label="Type of descriptor or fingerprint" help="Default is rdkit"> + <option value="rdkit" selected="true">rdkit</option> + <option value="maccs">maccs</option> + <option value="morgan2">morgan2</option> + <option value="morgan3">morgan3</option> + </param> + <param name="metric_opts" type="select" label="Similarity metric" help="Default is the Tanimoto coefficient"> + <option value="tanimoto" selected="true">tanimoto</option> + <option value="asymmetric">asymmetric</option> + <option value="braunblanquet">braunblanquet</option> + <option value="cosine">cosine</option> + <option value="dice">dice</option> + <option value="kulczynski">kulczynski</option> + <option value="mcconnaughey">mcconnaughey</option> + <option value="rogotgoldberg">rogotgoldberg</option> + <option value="russel">russel</option> + <option value="sokal">sokal</option> + </param> + <param name="fragment_opts" type="select" optional="true" label="Find single fragment" help="Find single fragment if more than one (hac = biggest by heavy atom count, mw = biggest by mol weight )"> + <option value="hac">Biggest by heavy atom count</option> + <option value="mw">Biggest by molecular weight</option> + </param> + <param name="hac_min" type="integer" optional="true" label="Minimum heavy atom count" help="Minimum number of heavy atoms for a candidate to pass screening"/> + <param name="hac_max" type="integer" optional="true" label="Maximum heavy atom count" help="Maximum number of heavy atoms for a candidate to pass screening"/> + <param name="mw_min" type="float" optional="true" label="Minimum molecular weight" help="Minimum molecular weight for a candidate to pass screening"/> + <param name="mw_max" type="float" optional="true" label="Maximum molecular weight" help="Maximum molecular weight for a candidate to pass screening"/> + </inputs> + + <expand macro="outputs" /> + + <tests> + <test> + <param name='comparator_opts' value="str"/> + <param name="input" value="C1N=C(C2=CC=CC=C2)C2=CC=CC=C2C2=C1C=NC(NC1=CC=CC=C1)=N2"/> + <param name="infile" value="dhfr_3d.sdf" ftype="sdf"/> + <param name="descriptor_opts" value="rdkit" /> + <param name="metric_opts" value="tanimoto" /> + <param name="sim_min" value="0.45" /> + <param name="sim_max" value="1.0" /> + <output name="outfile" ftype='sdf' file="screen_output1.sdf"/> + </test> + <test> + <param name='comparator_opts' value="file"/> + <param name="input" value="pyrimethamine.mol" ftype="mol"/> + <param name="infile" value="dhfr_3d.sdf" ftype="sdf"/> + <param name="descriptor_opts" value="rdkit" /> + <param name="metric_opts" value="tanimoto" /> + <param name="sim_min" value="0.7" /> + <param name="sim_max" value="0.8" /> + <output name="outfile" ftype='sdf' file="screen_output2.sdf"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What this tool does** + +Screen a library against a compound, filtering by fingerprint similarity and a number of other properties. + +.. class:: infomark + +**Input** + +| - Compound library in `SDF Format`_ +| - Compound to screen against in `SMILES`_ or `SDF Format`_ +| - Type of fingerprint +| - Required molecular weight and heavy atom count + +.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification + +----- + +.. class:: infomark + + **Output** + +SD-file of screened compounds, with new 'Similarity' property. + +]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file