Mercurial > repos > bgruening > ctb_im_standardize
comparison standardize.xml @ 0:fbfac03ce8c3 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
author | bgruening |
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date | Tue, 21 Jul 2020 05:24:19 -0400 |
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-1:000000000000 | 0:fbfac03ce8c3 |
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1 <tool id="ctb_im_standardize" name="Standardize SD-files" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | |
2 <description>using RDKit</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 <token name="@GALAXY_VERSION@">0</token> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 standardize | |
10 -i '$infile' | |
11 -if sdf | |
12 $fragment_opts | |
13 $neutralize | |
14 --meta | |
15 -o outp &>> $logfile && | |
16 cat outp_metrics.txt &>> $logfile && | |
17 gzip -d outp.sdf.gz | |
18 ]]></command> | |
19 <inputs> | |
20 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/> | |
21 <param name="fragment_opts" type="select" label="Fragment" help="The approach for choosing the largest fragment; alternatively the whole molecule is used."> | |
22 <option value="" selected="true">Use whole molecule</option> | |
23 <option value="--fragment-method hac">Biggest by heavy atom count</option> | |
24 <option value="--fragment-method mw">Biggest by molecular weight</option> | |
25 </param> | |
26 <param name="neutralize" type="boolean" label="Neutralize" truevalue="--neutralize" falsevalue="" help="Remove any charge from the molecule"/> | |
27 </inputs> | |
28 | |
29 <expand macro="outputs" /> | |
30 | |
31 <tests> | |
32 <test> | |
33 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> | |
34 <param name="fragment_opts" value="--fragment-method hac"/> | |
35 <output name="outfile" ftype='sdf' file="standardize_output1.sdf"/> | |
36 </test> | |
37 <test> | |
38 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> | |
39 <param name="fragment_opts" value="--fragment-method mw"/> | |
40 <param name="neutralize" value="true"/> | |
41 <output name="outfile" ftype='sdf' file="standardize_output2.sdf"/> | |
42 </test> | |
43 </tests> | |
44 <help><![CDATA[ | |
45 | |
46 .. class:: infomark | |
47 | |
48 **What this tool does** | |
49 | |
50 Standardizes an SD-file using RDKit. | |
51 | |
52 .. class:: infomark | |
53 | |
54 **Input** | |
55 | |
56 | - Input file in `SDF Format`_ | |
57 | |
58 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file | |
59 .. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification | |
60 | |
61 ----- | |
62 | |
63 .. class:: infomark | |
64 | |
65 **Output** | |
66 | |
67 SD-file of standardized compounds. | |
68 | |
69 ]]></help> | |
70 <expand macro="citations" /> | |
71 </tool> |