annotate change_title_to_metadata_value.xml @ 16:a638d8d13bb3 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:02:57 +0000
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1 <tool id="openbabel_change_title" name="Change title" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>to metadata 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@">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 python '$__tool_directory__/change_title_to_metadata_value.py'
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12 --infile '${infile}'
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13 --key '${key}'
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14 --outfile '${outfile}'
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15 $random
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param name="infile" type="data" format="sdf,mol2" label="Compound file" help="Specify a compound file in SDF or MOL2 format."/>
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20 <param name="key" type="text" format="text" label="Compound identifier encoded in the SD-file." help="Specify the key name of the SDF metadata which contains the molecule identifier (e.g. 'PUBCHEM_SHAPE_VOLUME')"/>
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21 <param name="random" type="boolean" truevalue="--random" falsevalue="" label="Add a random suffix to the title"
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22 help="The title will be named like TITLE__xbrsjqssafh2t"/>
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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" ftype="sdf" value="CID_3033.sdf"/>
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30 <param name="key" value="PUBCHEM_SHAPE_VOLUME"/>
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31 <output name="outfile" ftype="sdf" file="change_title_on_CID_3033.sdf" lines_diff="2"/>
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32 </test>
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33 <test>
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34 <param name="infile" ftype="sdf" value="transfs.sdf"/>
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35 <param name="key" value="Name"/>
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36 <param name="random" value="true"/>
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37 <output name="outfile" ftype="sdf">
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38 <assert_contents>
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39 <has_text_matching expression="NC\(=NO\)NCCc1ccc\(S\(N\)\(=O\)=O\)cc1__(.*){13}" />
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40 </assert_contents>
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41 </output>
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42 </test>
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43 </tests>
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44 <help>
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45 <![CDATA[
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46
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47 .. class:: infomark
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48
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49 **What this tool does**
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50
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51 Reassigns the title of a molecule file (SDF or MOL2) to a metadata value of a given ID in the same molecule file. For example, if the metadata identifier chosen is PUBCHEM_SHAPE_VOLUME, then the title of the file (in the first line) will be replaced by the variable listed under PUBCHEM_SHAPE_VOLUME.
0
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52
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53 -----
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54
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55 .. class:: infomark
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56
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57 **Input**
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58
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59 `SD-file`_ with metadata including the given ID.
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60
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61 .. _SD-file: http://en.wikipedia.org/wiki/Chemical_table_file
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62
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63 -----
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64
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65 .. class:: infomark
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66
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67 **Output**
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68
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69 Same as input, with changed title tag.
0
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72 ]]>
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73 </help>
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74 <expand macro="citations"/>
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75 </tool>