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comparison chemfp_sdf2fps/sdf2fps.xml @ 1:43a9e7d9b24f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
author bgruening
date Sun, 01 Nov 2015 10:27:01 -0500
parents 354d3c6bb894
children
comparison
equal deleted inserted replaced
0:354d3c6bb894 1:43a9e7d9b24f
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.1p1">chemfp</requirement> 5 <requirement type="package" version="1.1p1">chemfp</requirement>
6 <requirement type="package" version="2.3.2">openbabel</requirement> 6 <requirement type="package" version="2.3.2">openbabel</requirement>
7 </requirements> 7 </requirements>
8 <command> 8 <command>
9 <![CDATA[
9 sdf2fps --pubchem "${infile}" > "${outfile}" 10 sdf2fps --pubchem "${infile}" > "${outfile}"
11 ]]>
10 </command> 12 </command>
11 <inputs> 13 <inputs>
12 <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/> 14 <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/>
13 </inputs> 15 </inputs>
14 <outputs> 16 <outputs>
15 <data name="outfile" format="fps"/> 17 <data name="outfile" format="fps"/>
16 </outputs> 18 </outputs>
17 <tests> 19 <tests>
18 </tests> 20 </tests>
19 <help> 21 <help>
22 <![CDATA[
20 23
21 .. class:: infomark 24 .. class:: infomark
22 25
23 **What this tool does** 26 **What this tool does**
24 27
33 `SD-Format`_ 36 `SD-Format`_
34 37
35 .. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file 38 .. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file
36 39
37 * Example:: 40 * Example::
38 41
39 28434379 42 28434379
40 -OEChem-02031205132D 43 -OEChem-02031205132D
41 44
42 37 39 0 0 0 0 0 0 0999 V2000 45 37 39 0 0 0 0 0 0 0999 V2000
43 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 46 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
44 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 47 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
45 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 48 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
46 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 49 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
47 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 50 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
48 7.3704 0.9433 0.0000 C 0 0 0 0 51 7.3704 0.9433 0.0000 C 0 0 0 0
49 ...... 52 ......
50 1 15 1 0 0 0 0 53 1 15 1 0 0 0 0
51 1 35 1 0 0 0 0 54 1 35 1 0 0 0 0
52 2 5 1 0 0 0 0 55 2 5 1 0 0 0 0
53 2 11 1 0 0 0 0 56 2 11 1 0 0 0 0
55 3 12 2 0 0 0 0 58 3 12 2 0 0 0 0
56 3 13 1 0 0 0 0 59 3 13 1 0 0 0 0
57 4 18 1 0 0 0 0 60 4 18 1 0 0 0 0
58 ...... 61 ......
59 62
60 &gt;PUBCHEM_COMPOUND_CID&lt; 63 >PUBCHEM_COMPOUND_CID<
61 28434379 64 28434379
62 65
63 &gt; &lt;PUBCHEM_COMPOUND_CANONICALIZED&gt; 66 > <PUBCHEM_COMPOUND_CANONICALIZED>
64 1 67 1
65 68
66 &gt; &lt;PUBCHEM_CACTVS_COMPLEXITY&gt; 69 > <PUBCHEM_CACTVS_COMPLEXITY>
67 280 70 280
68 71
69 &gt; &lt;PUBCHEM_CACTVS_HBOND_ACCEPTOR&gt; 72 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
70 2 73 2
71 74
72 &gt; &lt;PUBCHEM_CACTVS_HBOND_DONOR&gt; 75 > <PUBCHEM_CACTVS_HBOND_DONOR>
73 2 76 2
74 77
75 &gt; &lt;PUBCHEM_CACTVS_ROTATABLE_BOND&gt; 78 > <PUBCHEM_CACTVS_ROTATABLE_BOND>
76 2 79 2
77 80
78 &gt; &lt;PUBCHEM_CACTVS_SUBSKEYS&gt; 81 > <PUBCHEM_CACTVS_SUBSKEYS>
79 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA== 82 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
80 83
81 &gt; 84 >
82 85
83 ----- 86 -----
84 87
85 .. class:: infomark 88 .. class:: infomark
86 89
109 chemfp_ project 112 chemfp_ project
110 113
111 .. _chemfp: http://chemfp.com/ 114 .. _chemfp: http://chemfp.com/
112 115
113 116
117 ]]>
114 </help> 118 </help>
115 </tool> 119 </tool>