Mercurial > repos > bgruening > ctb_im_pbf_ev
comparison pbf_ev.xml @ 0:38b8e1d2bb78 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
author | bgruening |
---|---|
date | Tue, 21 Jul 2020 05:26:38 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:38b8e1d2bb78 |
---|---|
1 <tool id="ctb_im_pbf_ev" name="Calculate plane of best fit for molecules" 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 pbf_ev | |
10 -i '$infile' | |
11 -if sdf | |
12 --meta | |
13 -of sdf | |
14 -o outp &>> $logfile && | |
15 ##cat outp_metrics.txt &>> $logfile && | |
16 gzip -d outp.sdf.gz | |
17 ]]></command> | |
18 <inputs> | |
19 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/> | |
20 </inputs> | |
21 | |
22 <expand macro="outputs" /> | |
23 | |
24 <tests> | |
25 <test> | |
26 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> | |
27 <output name="logfile"> | |
28 <assert_contents> | |
29 <has_text text="Handled 36 molecules, resulting in 36 outputs"/> | |
30 </assert_contents> | |
31 </output> | |
32 </test> | |
33 </tests> | |
34 <help><![CDATA[ | |
35 | |
36 .. class:: infomark | |
37 | |
38 **What this tool does** | |
39 | |
40 Calculate plane of best fit for molecules. | |
41 | |
42 .. class:: infomark | |
43 | |
44 **Input** | |
45 | |
46 | - Input file in `SDF Format`_ | |
47 | |
48 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file | |
49 .. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification | |
50 | |
51 ----- | |
52 | |
53 .. class:: infomark | |
54 | |
55 **Output** | |
56 | |
57 SD-file with plane of best fit. | |
58 | |
59 ]]></help> | |
60 <expand macro="citations"/> | |
61 </tool> |