Mercurial > repos > bgruening > rxdock_sort_filter
comparison sort_filter.xml @ 0:475cde209992 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
author | bgruening |
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date | Sat, 04 Apr 2020 15:08:15 -0400 |
parents | |
children | 7be0793dd448 |
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1 <tool id="rxdock_sort_filter" name="SDF sort and filter" version="0.1.0"> | |
2 <description>using the sdsort provided with rxDock</description> | |
3 <macros> | |
4 <import>rdock_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command><![CDATA[ | |
8 | |
9 sdsort -n $descending -s -f'$sort_field' -id'$name_field' '$input' | | |
10 sdfilter -f'\$_COUNT <= $top' -s'$name_field' | | |
11 sdsort -n $descending -f'$sort_field' > '$output' | |
12 | |
13 ]]></command> | |
14 | |
15 <inputs> | |
16 <param type="data" name="input" format="sdf" label="Molecules" help="Molecules in SDF format"/> | |
17 <param name="top" type="integer" value="1" label="Number of records to keep in output" help="Number of best scoring records to keep"/> | |
18 <param name="sort_field" type="text" label="Field to sort on" optional="false" help="Name of the field to sort records by"> | |
19 <sanitizer> | |
20 <valid initial="string.printable"> | |
21 <remove value="'"/> | |
22 </valid> | |
23 <mapping initial="none"/> | |
24 </sanitizer> | |
25 </param> | |
26 <param name="name_field" type="text" label="Grouping field name" optional="false" help="Name of the field to group records by (must be sequential)"> | |
27 <sanitizer> | |
28 <valid initial="string.printable"> | |
29 <remove value="'"/> | |
30 </valid> | |
31 <mapping initial="none"/> | |
32 </sanitizer> | |
33 </param> | |
34 <param name="descending" type="boolean" label="Sort descending" truevalue="-r" falsevalue="" checked="true" | |
35 help="Generate the name field (first line) for cases where this is empty"/> | |
36 </inputs> | |
37 <outputs> | |
38 <data name="output" format="sdf" label="SDF sort+filter on ${on_string}"/> | |
39 </outputs> | |
40 <tests> | |
41 <test> | |
42 <param name="input" value="poses.sdf"/> | |
43 <param name="sort_field" value="TransFSScore"/> | |
44 <param name="name_field" value="Name"/> | |
45 <output name="output" file="poses-descending.sdf" ftype="sdf" /> | |
46 </test> | |
47 <test> | |
48 <param name="input" value="poses.sdf"/> | |
49 <param name="sort_field" value="TransFSScore"/> | |
50 <param name="name_field" value="Name"/> | |
51 <param name="descending" value="False"/> | |
52 <output name="output" file="poses-ascending.sdf" ftype="sdf" /> | |
53 </test> | |
54 </tests> | |
55 <help><![CDATA[ | |
56 | |
57 .. class:: infomark | |
58 | |
59 This tool sorts and filters SD files using the sdsort and sdfilter tools from the rxDock suite. | |
60 See https://www.rxdock.org for more details about rxDock and associated programs. | |
61 The expected use is for filtering and sorting virtual screening results such as docking. | |
62 | |
63 ----- | |
64 | |
65 .. class:: infomark | |
66 | |
67 **Inputs** | |
68 An SD-file, together with names of fields to sort and group records by, and the number of records to appear in the output. | |
69 The sorting is performed on groups of molecules, with the group being identified by a field in the SDF (the name_field | |
70 parameter). Records from a group MUST be sequential. | |
71 The records within each group are sorted by the value of a field in the SDF (the sort_field parameter) and you can | |
72 specify ascending or descending order (the descending parameter). | |
73 Finally a number of top scoring (the top parameter, typically having a value of 1) are written to the output. | |
74 | |
75 ----- | |
76 | |
77 .. class:: infomark | |
78 | |
79 **Outputs** | |
80 An SD-file, containing molecules filtered by the field specified. | |
81 | |
82 ]]></help> | |
83 <expand macro="citations"/> | |
84 </tool> |