Mercurial > repos > bgruening > openbabel_change_title
annotate change_title_to_metadata_value.xml @ 10:eed751918a20 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
author | bgruening |
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date | Sat, 21 Mar 2020 10:26:59 -0400 |
parents | 9c15e92bed39 |
children | 3ecaa9634126 |
rev | line source |
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10
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
parents:
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1 <tool id="openbabel_change_title" name="Change title" version="@VERSION@.1"> |
7
9c15e92bed39
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
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2 <description>to metadata value.</description> |
0
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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4 <macros> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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5 <import>macros.xml</import> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
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6 </macros> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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7 <expand macro="requirements"/> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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8 <command detect_errors="aggressive"> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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9 <![CDATA[ |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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10 python '$__tool_directory__/change_title_to_metadata_value.py' |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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11 --infile '${infile}' |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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12 --key '${key}' |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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13 --outfile '${outfile}' |
10
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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14 $random |
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fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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15 ]]> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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16 </command> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
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17 <inputs> |
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9c15e92bed39
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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18 <param name="infile" type="data" format="sdf,mol2" label="Compound file" help="Specify a compound file in SDF or MOL2 format."/> |
9c15e92bed39
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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19 <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')"/> |
10
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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20 <param name="random" type="boolean" truevalue="--random" falsevalue="" label="Add a random suffix to the title" |
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
parents:
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21 help="The title will be named like TITLE__xbrsjqssafh2t"/> |
0
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
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22 </inputs> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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23 <outputs> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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24 <expand macro="output_like_input"/> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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25 </outputs> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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26 <tests> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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27 <test> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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28 <param name="infile" ftype="sdf" value="CID_3033.sdf"/> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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29 <param name="key" value="PUBCHEM_SHAPE_VOLUME"/> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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30 <output name="outfile" ftype="sdf" file="change_title_on_CID_3033.sdf" lines_diff="2"/> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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31 </test> |
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eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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32 <test> |
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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33 <param name="infile" ftype="sdf" value="transfs.sdf"/> |
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
parents:
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34 <param name="key" value="Name"/> |
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
parents:
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35 <param name="random" value="true"/> |
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
parents:
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36 <output name="outfile" ftype="sdf"> |
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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37 <assert_contents> |
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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38 <has_text_matching expression="NC\(=NO\)NCCc1ccc\(S\(N\)\(=O\)=O\)cc1__(.*){13}" /> |
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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39 </assert_contents> |
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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40 </output> |
eed751918a20
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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41 </test> |
0
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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42 </tests> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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43 <help> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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44 <![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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45 |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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46 .. class:: infomark |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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47 |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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48 **What this tool does** |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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49 |
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9c15e92bed39
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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50 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
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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51 |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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52 ----- |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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53 |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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54 .. class:: infomark |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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55 |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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56 **Input** |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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57 |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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58 `SD-file`_ with metadata including the given ID. |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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59 |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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60 .. _SD-file: http://en.wikipedia.org/wiki/Chemical_table_file |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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61 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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62 ----- |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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63 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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64 .. class:: infomark |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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65 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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66 **Output** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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67 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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68 Same as input, with changed title tag. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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69 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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70 |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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71 ]]> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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72 </help> |
fd7097abe45a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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73 <expand macro="citations"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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74 </tool> |