Mercurial > repos > bgruening > openbabel_remduplicates
view ob_remDuplicates.xml @ 13:12aca74f07d7 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author | bgruening |
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date | Mon, 19 Oct 2020 14:47:33 +0000 |
parents | 50ca8845e7f5 |
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<tool id="openbabel_remDuplicates" name="Remove duplicated molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>from a library of compounds</description> <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> <macros> <import>macros.xml</import> <token name="@GALAXY_VERSION@">0</token> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"> <![CDATA[ obabel -i"${infile.ext}" "${infile}" -ocopy --unique "${descriptor}" -O "${outfile}" -e ]]> </command> <inputs> <expand macro="infile_all_types"/> <param name="descriptor" type="select" label="Select descriptor for molecule comparison"> <option value="inchi" selected="True">InChI (default)</option> <option value="cansmi">Canonical SMILES</option> <option value="cansmiNS">Canonical SMILES (without stereo)</option> </param> </inputs> <outputs> <expand macro="output_like_input"/> </outputs> <tests> <test> <param name="infile" ftype="smi" value="2_mol.smi"/> <param name="descriptor" value="inchi" /> <output name="outfile" ftype="smi" file="ob_remDuplicates_on_2_mol.smi" /> </test> </tests> <help> <![CDATA[ .. class:: infomark **What this tool does** Filters a library of compounds and removes duplicated molecules. ----- .. class:: warningmark **Hint** Comparison based on Canonical SMILES without stereochemistry may be useful in cases where this information is not crucial for library preparation. Several VS tools will automatically generate stereoisomeric forms. ----- .. class:: infomark **Input** | - `InChI`_ | - `SMILES Format`_ .. _InChI: https://en.wikipedia.org/wiki/International_Chemical_Identifier .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification ----- .. class:: infomark **Output** Same as input format. ]]> </help> <expand macro="citations"/> </tool>