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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
author bgruening
date Mon, 22 May 2017 03:01:21 -0400
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1 <tool id="ctb_stripit" name="Strip-it" version="1.0.2.1">
2 <description>extracts predefined scaffolds from molecules</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <requirements>
5 <requirement type="package" version="1.0.2">strip_it</requirement>
6 </requirements>
7 <command detect_errors="aggressive">
8 <![CDATA[
9 ln -s '$infile' '$infile.${infile.ext}' &&
10 strip-it
11 --input '$infile.${infile.ext}'
12 --output '$outfile'
13 --noLog
14 $noHeader
15 ]]>
16 </command>
17 <inputs>
18 <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
19 <param argument='--noHeader' type='boolean' truevalue='--noHeader' falsevalue=''
20 label='Do not print a header in the output file' />
21
22 </inputs>
23 <outputs>
24 <data name="outfile" format="tabular" />
25 </outputs>
26 <tests>
27 <test>
28 <param name="infile" ftype="sdf" value="CID_3037.sdf"/>
29 <param name="noHeader" value="false"/>
30 <output name="outfile" file="Strip-it_on_CID3037.tabular" />
31 </test>
32 </tests>
33 <help>
34 <![CDATA[
35
36
37 .. class:: infomark
38
39 **What this tool does**
40
41 Strip-it is a program that extracts predefined scaffolds from organic small
42 molecules.
43
44 The program comes with a number of predefined molecular scaffolds for
45 extraction. These scaffolds include, amongst others
46
47 - `molecular frameworks`_ as originally described by Bemis and Murcko
48 - `molecular frameworks and the reduced molecular frameworks`_ as described by Ansgar Schuffenhauer and coworkers
49 - `scaffold topologies`_ as described by Sara Pollock and coworkers
50
51 .. _molecular frameworks: http://www.ncbi.nlm.nih.gov/pubmed/8709122
52 .. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf
53 .. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680
54
55 -----
56
57 .. class:: infomark
58
59
60 **Input**
61
62 | - `SD-Format`_
63 | - `SMILES Format`_
64 | - `MOL2 Format`_
65
66 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
67 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
68 .. _MOL2 Format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
69
70
71 -----
72
73 .. class:: infomark
74
75 **Output**
76
77 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
78 | NAME | MOLECULE | RINGS_WITH_LINKERS_1 | RINGS_WITH_LINKERS_2 | MURCKO_1 | ... |
79 +=============+================================+======================+========================+======================+=====+
80 | Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1 | c1ccc(cc1)Nc1ccccc1 | C1CCC(CC1)CC1CCCCC1 | ... |
81 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
82 | Bupivacaine | CCCCN1CCCCC1C(=O)Nc1c(C)cccc1C | C1CCC(NC1)CNc1ccccc1 | O=C(C1CCCCN1)Nc1ccccc1 | C1CCC(CC1)CCC1CCCCC1 | ... |
83 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
84 | ... | ... | ... | ... | ... | ... |
85 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
86
87 -----
88
89 .. class:: infomark
90
91 **Cite**
92
93 `Silicos-it`_ - strip-it
94
95 .. _Silicos-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/strip-it/1.0.2/strip-it.html
96
97
98 ]]>
99 </help>
100 <citations>
101 </citations>
102 </tool>