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comparison macros_packmol.xml @ 0:0b8a0ce446f5 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
author chemteam
date Mon, 08 Oct 2018 05:31:29 -0400
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children 539fb45630e6
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-1:000000000000 0:0b8a0ce446f5
1 <macros>
2 <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format.">
3 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
4 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
5 <section name="structureparams" title="Structure Parameters (Make Changes!)" expanded="false">
6 <param name="number" type="integer" multiple="True" value="100" />
7 <param name="radius" type="float" multiple="True" value="1.0" />
8 <param name="resnumbers" type="integer" multiple="True" value="0" help="Default is to number 1 to n for type 1 and 1 to n for type 2"/>
9 <repeat name="constraints_repeat" min="1" max="3" title="Select constraint(s) to apply:">
10 <conditional name="constraints">
11 <param name="constraint" type="select" label="Shape Constraint selection" help="Choose the constraint for the molecules">
12 <option value="fixed">fixed - hold 1 molecule in fixed position (hardcoded number=1) Exclusive other constraints not possible</option>
13 <option selected="True" value="cube">cube</option>
14 <option value="box">box</option>
15 <option value="sphere">sphere</option>
16 <option value="ellipsoid">ellipsoid </option>
17 <option value="plane">plane</option>
18 <option value="cylinder">cylinder</option>
19 </param>
20 <when value="fixed">
21 <param name="center" type="select" label="Center" help="center">
22 <option value="Yes">yes</option>
23 <option value="No">no</option>
24 </param>
25 <param name="x" type="float" value="0.0" label="x" />
26 <param name="y" type="float" value="0.0" label="y" />
27 <param name="z" type="float" value="0.0" label="z" />
28 <param name="a" type="float" value="0.0" label="a" />
29 <param name="b" type="float" value="0.0" label="b" />
30 <param name="g" type="float" value="0.0" label="g" />
31 </when>
32 <when value="cube">
33 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
34 <option value="inside">inside</option>
35 <option value="outside">outside</option>
36 </param>
37 <param name="xmin" type="float" value="0.0" label="xmin" />
38 <param name="ymin" type="float" value="0.0" label="ymin" />
39 <param name="zmin" type="float" value="0.0" label="zmin" />
40 <param name="d" type="float" value="40.0" label="d" />
41 </when>
42 <when value="box">
43 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
44 <option value="inside">inside</option>
45 <option value="outside">outside</option>
46 </param>
47 <param name="xmin" type="float" value="0.0" label="xmin" />
48 <param name="ymin" type="float" value="0.0" label="ymin" />
49 <param name="zmin" type="float" value="0.0" label="zmin" />
50 <param name="xmax" type="float" value="40.0" label="xmax" />
51 <param name="ymax" type="float" value="40.0" label="ymax" />
52 <param name="zmax" type="float" value="40.0" label="zmax" />
53 </when>
54 <when value="sphere">
55 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
56 <option value="inside">inside</option>
57 <option value="outside">outside</option>
58 </param>
59 <param name="a" type="float" value="0.0" label="a" />
60 <param name="b" type="float" value="0.0" label="b" />
61 <param name="c" type="float" value="0.0" label="c" />
62 <param name="d" type="float" value="40.0" label="d" />
63 </when>
64 <when value="ellipsoid">
65 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
66 <option value="inside">inside</option>
67 <option value="outside">outside</option>
68 </param>
69 <param name="a1" type="float" value="0.0" label="a1" />
70 <param name="b1" type="float" value="0.0" label="b1" />
71 <param name="c1" type="float" value="0.0" label="c1" />
72 <param name="a2" type="float" value="20.0" label="a2" />
73 <param name="b2" type="float" value="20.0" label="b2" />
74 <param name="c2" type="float" value="20.0" label="c2" />
75 <param name="d" type="float" value="40.0" label="d" />
76 </when>
77 <when value="plane">
78 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
79 <option value="over">over</option>
80 <option value="below">below</option>
81 </param>
82 <param name="a" type="float" value="0.0" label="a" />
83 <param name="b" type="float" value="0.0" label="b" />
84 <param name="c" type="float" value="0.0" label="c" />
85 <param name="d" type="float" value="10.0" label="d" />
86 </when>
87 <when value="cylinder">
88 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
89 <option value="inside">inside</option>
90 <option value="outside">outside</option>
91 </param>
92 <param name="a1" type="float" value="0.0" label="a1" />
93 <param name="b1" type="float" value="0.0" label="b1" />
94 <param name="c1" type="float" value="0.0" label="c1" />
95 <param name="a2" type="float" value="40.0" label="a2" />
96 <param name="b2" type="float" value="40.0" label="b2" />
97 <param name="c2" type="float" value="40.0" label="c2" />
98 <param name="d" type="float" value="10.0" label="d" />
99 <param name="l" type="float" value="10.0" label="l" />
100 </when>
101 </conditional>
102 </repeat>
103 </section>
104 </repeat>
105 </xml>
106 </macros>