Mercurial > repos > bgruening > openbabel_change_title
comparison 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 |
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9:f924a1728291 | 10:eed751918a20 |
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1 <tool id="openbabel_change_title" name="Change title" version="@VERSION@.0"> | 1 <tool id="openbabel_change_title" name="Change title" version="@VERSION@.1"> |
2 <description>to metadata value.</description> | 2 <description>to metadata value.</description> |
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> | 3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> |
4 <macros> | 4 <macros> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
9 <![CDATA[ | 9 <![CDATA[ |
10 python '$__tool_directory__/change_title_to_metadata_value.py' | 10 python '$__tool_directory__/change_title_to_metadata_value.py' |
11 --infile '${infile}' | 11 --infile '${infile}' |
12 --key '${key}' | 12 --key '${key}' |
13 --outfile '${outfile}' | 13 --outfile '${outfile}' |
14 $random | |
14 ]]> | 15 ]]> |
15 </command> | 16 </command> |
16 <inputs> | 17 <inputs> |
17 <param name="infile" type="data" format="sdf,mol2" label="Compound file" help="Specify a compound file in SDF or MOL2 format."/> | 18 <param name="infile" type="data" format="sdf,mol2" label="Compound file" help="Specify a compound file in SDF or MOL2 format."/> |
18 <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')"/> | 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')"/> |
20 <param name="random" type="boolean" truevalue="--random" falsevalue="" label="Add a random suffix to the title" | |
21 help="The title will be named like TITLE__xbrsjqssafh2t"/> | |
19 </inputs> | 22 </inputs> |
20 <outputs> | 23 <outputs> |
21 <expand macro="output_like_input"/> | 24 <expand macro="output_like_input"/> |
22 </outputs> | 25 </outputs> |
23 <tests> | 26 <tests> |
24 <test> | 27 <test> |
25 <param name="infile" ftype="sdf" value="CID_3033.sdf"/> | 28 <param name="infile" ftype="sdf" value="CID_3033.sdf"/> |
26 <param name="key" value="PUBCHEM_SHAPE_VOLUME"/> | 29 <param name="key" value="PUBCHEM_SHAPE_VOLUME"/> |
27 <output name="outfile" ftype="sdf" file="change_title_on_CID_3033.sdf" lines_diff="2"/> | 30 <output name="outfile" ftype="sdf" file="change_title_on_CID_3033.sdf" lines_diff="2"/> |
31 </test> | |
32 <test> | |
33 <param name="infile" ftype="sdf" value="transfs.sdf"/> | |
34 <param name="key" value="Name"/> | |
35 <param name="random" value="true"/> | |
36 <output name="outfile" ftype="sdf"> | |
37 <assert_contents> | |
38 <has_text_matching expression="NC\(=NO\)NCCc1ccc\(S\(N\)\(=O\)=O\)cc1__(.*){13}" /> | |
39 </assert_contents> | |
40 </output> | |
28 </test> | 41 </test> |
29 </tests> | 42 </tests> |
30 <help> | 43 <help> |
31 <![CDATA[ | 44 <![CDATA[ |
32 | 45 |