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comparison sdf2fps.xml @ 7:0d88631bb7de draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:32:50 -0400
parents 70b071de9bee
children 92c7cdc243e8
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6:e3a7d6cc87af 7:0d88631bb7de
1 <tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="0.2"> 1 <tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="1.5">
2 <description>extract fingerprints from sdf files metadata</description> 2 <description>- extract fingerprints from sdf file metadata</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> 3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.1p1">chemfp</requirement> 5 <requirement type="package" version="1.5">chemfp</requirement>
6 <requirement type="package" version="2.4.1">openbabel</requirement> 6 <requirement type="package" version="2.4.1">openbabel</requirement>
7 </requirements> 7 </requirements>
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 sdf2fps --pubchem '${infile}' > '${outfile}' 10 sdf2fps --pubchem '${infile}' > '${outfile}'
11 ]]> 11 ]]>
12 </command> 12 </command>
13 <inputs> 13 <inputs>
14 <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/> 14 <param name="infile" type='data' format="sdf" label="SD-file with fingerprints as metadata"/>
15 </inputs> 15 </inputs>
16 <outputs> 16 <outputs>
17 <data name="outfile" format="fps"/> 17 <data name="outfile" format="fps"/>
18 </outputs> 18 </outputs>
19 <tests> 19 <tests>
35 35
36 .. class:: infomark 36 .. class:: infomark
37 37
38 **Input** 38 **Input**
39 39
40 `SD-Format`_ 40 `SD-Format`_, storing the atom types, together with the Cartesian coordinates.
41 41
42 .. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file 42 .. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file
43 43
44 * Example:: 44 * Example::
45 45
91 91
92 .. class:: infomark 92 .. class:: infomark
93 93
94 **Output** 94 **Output**
95 95
96 After the first few lines, starting with a hash symbol, which contain generic information, the fingerprints are listed as hexadecimal strings.
97
96 * Example:: 98 * Example::
97 99
98 #FPS1 100 #FPS1
99 #num_bits=881 101 #num_bits=881
100 #type=CACTVS-E_SCREEN/1.0 extended=2 102 #type=CACTVS-E_SCREEN/1.0 extended=2