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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 11:03:49 +0000
parents f697d9601273
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43167f164076 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="openbabel_addh" name="Add hydrogen atoms" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>at a certain pH value</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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6 <token name="@GALAXY_VERSION@">1</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 python $__tool_directory__/ob_addh.py
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12 -i "${infile}"
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13 --iformat "${infile.ext}"
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14 -o "${outfile}"
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15 $polar
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16 --pH "${pH_value}"
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17 ]]>
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18 </command>
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19 <inputs>
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20 <expand macro="infile_all_types_except_inchi"/>
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21 <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only (i.e. not to carbon atoms)"/>
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22 <param name="pH_value" type="float" value="7.4" min="0" max="14" label="Specify pH value"/>
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23 </inputs>
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24 <outputs>
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25 <expand macro="output_like_input"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="infile" value="CID_2244.can" ftype="smi" />
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30 <param name="polar" value="--polar" />
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31 <param name="pH_value" value="7.4" />
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32 <output name="outfile" file="CID_2244_addh.can" ftype="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 Parses a molecular file and adds hydrogen atoms at a user-defined pH value.
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44 * Protocol::
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45
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46 1. The hydrogen atoms included in the input molecule are deleted.
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47 2. Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.
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48
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49 -----
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50
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51 .. class:: infomark
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52
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53 **Input**
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54
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55 3D format files are required, e.g. SDF_
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57 .. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
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59 -----
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61 .. class:: warningmark
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62
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63 **Hint**
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64
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65 To avoid possible crashes, only molecules with more than five heavy atoms are parsed.
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66
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67 -----
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68
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69 .. class:: infomark
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71 **Output**
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73 Same output format as the input format.
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76 ]]>
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77 </help>
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78 <expand macro="citations">
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79 <citation type="doi">10.1186/1752-153X-2-5</citation>
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80 </expand>
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81 </tool>