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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:01:36 +0000
parents aebc671bae78
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aebc671bae78 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="openbabel_remSmall" name="Remove small molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>from a library of compounds</description>
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
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4 <macros>
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5 <import>macros.xml</import>
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aebc671bae78 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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6 <token name="@GALAXY_VERSION@">0</token>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 obabel
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12 -i"${infile.ext}"
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13 '${infile}'
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14 -ocopy
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15 -O '${outfile}'
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16 --filter "atoms > $cutoff"
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17 -e
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18 ]]>
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19 </command>
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20 <inputs>
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21 <expand macro="infile_all_types"/>
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22 <param name="cutoff" type="integer" value="5"
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23 label="Specify the cut-off value (only molecules with more than this number of atoms will pass the filter)" />
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24 </inputs>
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25 <outputs>
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26 <expand macro="output_like_input"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="infile" ftype="smi" value="3_mol.smi" />
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31 <param name="cutoff" value="5" />
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32 <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" />
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33 </test>
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34 </tests>
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35 <help>
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36 <![CDATA[
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37
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38 .. class:: infomark
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39
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40 **What this tool does**
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42 Filters a library of compounds and removes small molecules below a predefined input number of atoms.
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44 -----
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45
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46 .. class:: warningmark
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48 **Hint**
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49
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50 Some libraries may contain molecules without a 1D/3D descriptor, which may provoke crashes of any other tool. It is strongly advised to run this tool before proceeding to any further steps.
0
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51
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52 -----
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53
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54 .. class:: infomark
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55
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56 **Output**
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57
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58 Same as input format.
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59
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61
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62 ]]>
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63 </help>
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64 <expand macro="citations"/>
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65 </tool>