Mercurial > repos > bgruening > openbabel_remsmall
comparison ob_remSmall.xml @ 0:2704d4017b13 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
| author | bgruening |
|---|---|
| date | Sat, 20 May 2017 08:39:53 -0400 |
| parents | |
| children | c8d8caa9a54d |
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| -1:000000000000 | 0:2704d4017b13 |
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| 1 <tool id="openbabel_remSmall" name="Remove small molecules" version="@VERSION@.0"> | |
| 2 <description></description> | |
| 3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="aggressive"> | |
| 9 <![CDATA[ | |
| 10 obabel | |
| 11 -i"${infile.ext}" | |
| 12 '${infile}' | |
| 13 -ocopy | |
| 14 -O '${outfile}' | |
| 15 --filter "atoms > $cutoff" | |
| 16 -e | |
| 17 ]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <expand macro="infile_all_types"/> | |
| 21 <param name="cutoff" type="integer" value="5" | |
| 22 label="Specify the cut-off value (only molecules with more than this number of atoms will pass the filter)" /> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <expand macro="output_like_input"/> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test> | |
| 29 <param name="infile" ftype="smi" value="3_mol.smi" /> | |
| 30 <param name="cutoff" value="5" /> | |
| 31 <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" /> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help> | |
| 35 <![CDATA[ | |
| 36 | |
| 37 .. class:: infomark | |
| 38 | |
| 39 **What this tool does** | |
| 40 | |
| 41 Filters a library of compounds and removes small molecules below a predefined input number of atoms. | |
| 42 | |
| 43 ----- | |
| 44 | |
| 45 .. class:: warningmark | |
| 46 | |
| 47 **Hint** | |
| 48 | |
| 49 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. | |
| 50 | |
| 51 ----- | |
| 52 | |
| 53 .. class:: infomark | |
| 54 | |
| 55 **Output** | |
| 56 | |
| 57 Same as input format. | |
| 58 | |
| 59 | |
| 60 | |
| 61 ]]> | |
| 62 </help> | |
| 63 <expand macro="citations"/> | |
| 64 </tool> |