Mercurial > repos > bgruening > openbabel_remsmall
view ob_remSmall.xml @ 0:2704d4017b13 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author | bgruening |
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date | Sat, 20 May 2017 08:39:53 -0400 |
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children | c8d8caa9a54d |
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<tool id="openbabel_remSmall" name="Remove small molecules" version="@VERSION@.0"> <description></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> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"> <![CDATA[ obabel -i"${infile.ext}" '${infile}' -ocopy -O '${outfile}' --filter "atoms > $cutoff" -e ]]> </command> <inputs> <expand macro="infile_all_types"/> <param name="cutoff" type="integer" value="5" label="Specify the cut-off value (only molecules with more than this number of atoms will pass the filter)" /> </inputs> <outputs> <expand macro="output_like_input"/> </outputs> <tests> <test> <param name="infile" ftype="smi" value="3_mol.smi" /> <param name="cutoff" value="5" /> <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" /> </test> </tests> <help> <![CDATA[ .. class:: infomark **What this tool does** Filters a library of compounds and removes small molecules below a predefined input number of atoms. ----- .. class:: warningmark **Hint** Some libraries may contain molecules without a 1D/3D descriptor. These molecules may provoke crashes of any other tool. It is strongly adviced to run this tool before proceeding to any further steps. ----- .. class:: infomark **Output** Same as input format. ]]> </help> <expand macro="citations"/> </tool>