Mercurial > repos > bgruening > ctb_im_rxn_smarts_filter
comparison rxn_smarts_filter.xml @ 0:ce27129127e0 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
author | bgruening |
---|---|
date | Tue, 21 Jul 2020 05:26:16 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:ce27129127e0 |
---|---|
1 <tool id="ctb_im_rxn_smarts_filter" name="Reaction SMARTS filter" 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 rxn_smarts_filter | |
10 -i '$infile' | |
11 -if sdf | |
12 $multi | |
13 --meta | |
14 -of sdf | |
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="multi" type="boolean" label="Multi mode" truevalue="--multi" falsevalue="" help="Output one file for each reaction"/> | |
22 </inputs> | |
23 <outputs> | |
24 <data name="outfile" format="sdf" label="SDF output for ${tool.name}" from_work_dir="outp.sdf"/> | |
25 <data name="logfile" format="txt" label="Logfile for ${tool.name}"/> | |
26 <collection name="output_list" type="list"> | |
27 <filter>multi</filter> | |
28 <discover_datasets pattern="(?P<designation>.+)\.sdf$" ext="sdf" /> | |
29 </collection> | |
30 </outputs> | |
31 <tests> | |
32 <test> | |
33 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> | |
34 <param name="multi" value="" /> | |
35 <output name="outfile" ftype="sdf"> | |
36 <assert_contents> | |
37 <has_line line=" -5.0090 3.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0"/> | |
38 <has_line line="OB(O)c1nc(N2CCOCC2)c2oc3ncccc3c2n1"/> | |
39 <has_line line="CO[C@@H]1[C@H](NC(=O)c2ccccc2)C[C@H]2O[C@]1(C)n1c3ccccc3c3c4c(c5c6ccccc6n2c5c31)C(=O)NC4"/> | |
40 <has_text_matching expression="^([^\$]+?\$\$\$\$){36}?$"/> | |
41 </assert_contents> | |
42 </output> | |
43 <output name="logfile"> | |
44 <assert_contents> | |
45 <has_text text="Matched 36 molecules from a total of 36"/> | |
46 </assert_contents> | |
47 </output> | |
48 </test> | |
49 <test> | |
50 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> | |
51 <param name="multi" value="--multi" /> | |
52 <output name="outfile" ftype="sdf"> | |
53 <assert_contents> | |
54 <has_line line=" -5.0090 3.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0"/> | |
55 <has_line line="OB(O)c1nc(N2CCOCC2)c2oc3ncccc3c2n1"/> | |
56 <has_line line="CO[C@@H]1[C@H](NC(=O)c2ccccc2)C[C@H]2O[C@]1(C)n1c3ccccc3c3c4c(c5c6ccccc6n2c5c31)C(=O)NC4"/> | |
57 <has_text_matching expression="^([^\$]+?\$\$\$\$){36}?$"/> | |
58 </assert_contents> | |
59 </output> | |
60 <output name="logfile"> | |
61 <assert_contents> | |
62 <has_text text="Matched 36 molecules from a total of 36"/> | |
63 </assert_contents> | |
64 </output> | |
65 | |
66 <output_collection name="output_list" type="list"> | |
67 <element name="Sonogashira" ftype="sdf" > | |
68 <assert_contents> | |
69 <has_text text="COCCOc1cc2ncnc(Nc3cccc(C#C)c3)c2cc1OCCOC"/> | |
70 <has_text_matching expression="^([^\$]+?\$\$\$\$){1}?$"/> | |
71 </assert_contents> | |
72 </element> | |
73 </output_collection> | |
74 | |
75 </test> | |
76 </tests> | |
77 <help><![CDATA[ | |
78 ABCCDEFGHIJKLMNOPQRSTUVWXYZ | |
79 ]]></help> | |
80 <expand macro="citations" /> | |
81 </tool> |