annotate ob_addh.xml @ 4:b18b147b90fd draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c84729ec58f7f52d594066158afed175208d3d66
author bgruening
date Wed, 24 May 2017 10:01:57 -0400
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children d2e6d682bcd0
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1 <tool id="openbabel_addh" name="Add hydrogen atoms" version="@VERSION@.0">
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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 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive">
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9 <![CDATA[
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10 python $__tool_directory__/ob_addh.py
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11 -i "${infile}"
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12 --iformat "${infile.ext}"
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13 -o "${outfile}"
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14 $polar
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15 --pH "${pH_value}"
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16 ]]>
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17 </command>
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18 <inputs>
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19 <expand macro="infile_all_types"/>
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20 <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only"/>
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21 <param name="pH_value" type="float" value="7.4" min="0" max="14" label="Specify pH value"/>
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22 </inputs>
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23 <outputs>
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24 <expand macro="output_like_input"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="infile" value="CID_2244.can" ftype="smi" />
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29 <param name="polar" value="--polar" />
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30 <param name="pH_value" value="7.4" />
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31 <output name="outfile" file="CID_2244_addh.can" ftype="smi" />
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32 </test>
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33 </tests>
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34 <help>
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35 <![CDATA[
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36
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37 .. class:: infomark
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38
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39 **What this tool does**
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40
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41 Parses a molecular file and adds hydrogen atoms at a user-defined pH value.
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42
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43 * Protocol::
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44
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45 1. The hydrogen atoms included in the input molecule are deleted.
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46 2. Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.
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47
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48 -----
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49
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50 .. class:: infomark
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51
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52 **Input**
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53
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54 3D format files are required, e.g. SDF_
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55
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56 .. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
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57
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58 -----
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59
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60 .. class:: warningmark
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61
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62 **Hint**
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63
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64 To avoid possible crashes, only molecules with more than five heavy atoms are parsed.
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65
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66 -----
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67
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68 .. class:: infomark
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69
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70 **Output**
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71
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72 Same output format as the input format.
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73
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74
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75 ]]>
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76 </help>
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77 <expand macro="citations">
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78 <citation type="doi">10.1186/1752-153X-2-5</citation>
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79 </expand>
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80 </tool>