Mercurial > repos > guerler > spring_model

annotate macros.xml @ 2:3fd0f313665b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
author guerler
date Thu, 08 Apr 2021 18:23:33 +0000
parents 719931bce361
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
1 <macros>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
2 <xml name="requirements">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
3 <requirements>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
4 <requirement type="package" version="@TOOL_VERSION@">springsuite</requirement>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
5 <yield />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
6 </requirements>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
7 </xml>
1
719931bce361 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
8 <token name="@TOOL_VERSION@">0.2</token>
0
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
9 <token name="@VERSION_SUFFIX@">0</token>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
10
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
11 <xml name="ffindex_single_inputs">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
12 <param name="ffdata" type="data" format="ffdata" label="PDB Database" help="Database Data file." />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
13 <param name="ffindex" type="data" format="ffindex" label="PDB Database Index" help="Database Index file." />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
14 </xml>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
15
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
16 <xml name="ffindex_single_inputs_hhr">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
17 <param name="ffdata" type="data" format="ffdata" label="HHR Database" help="Database Data file." />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
18 <param name="ffindex" type="data" format="ffindex" label="HHR Database Index" help="Database Index file." />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
19 </xml>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
20
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
21 <xml name="citations">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
22 <citations>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
23 <citation type="doi">10.1021/ci300579r</citation>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
24 </citations>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
25 </xml>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
26 <xml name="logfile">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
27 <param name="logfile" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log file" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
28 </xml>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
29
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
30 <xml name="pdb_source">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
31 <conditional name="pdb_source">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
32 <param name="pdb_source_selector" type="select" label="Custom or built-in PDB" help="Built-ins have been indexed using ffindex">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
33 <option value="indexed" selected="true">Use a built-in index</option>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
34 <option value="history">Use a PDB index from history</option>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
35 </param>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
36 <when value="indexed">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
37 <param name="pdb" type="select" label="Select PDB database" help="">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
38 <options from_data_table="ffindex_indices">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
39 <filter type="sort_by" column="0" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
40 <filter type="static_value" column="3" value="pdb" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
41 <validator type="no_options" message="No indices are available" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
42 </options>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
43 </param>
1
719931bce361 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
44 <param name="zipped" type="select" label="Zipped entries in PDB database?" help="">
719931bce361 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
45 <option value="" selected="true">No</option>
719931bce361 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
46 <option value="gz">Yes</option>
719931bce361 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
47 </param>
0
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
48 </when>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
49 <when value="history">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
50 <expand macro="ffindex_single_inputs" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
51 </when>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
52 </conditional>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
53 </xml>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
54 <xml name="hhr_source">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
55 <conditional name="hhr_source">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
56 <param name="hhr_source_selector" type="select" label="Custom or built-in HHR index" help="Built-ins have been indexed using ffindex">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
57 <option value="indexed" selected="true">Use a built-in index</option>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
58 <option value="history">Use a HHR index from history</option>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
59 </param>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
60 <when value="indexed">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
61 <param name="hhr" type="select" label="Select HHR database" help="">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
62 <options from_data_table="ffindex_indices">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
63 <filter type="sort_by" column="0" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
64 <filter type="static_value" column="3" value="hhr" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
65 <validator type="no_options" message="No indices are available" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
66 </options>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
67 </param>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
68 </when>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
69 <when value="history">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
70 <expand macro="ffindex_single_inputs_hhr" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
71 </when>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
72 </conditional>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
73 </xml>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
74
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
75 <token name="@pdb_source@">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
76 #if $pdb_source.pdb_source_selector == 'indexed':
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
77 -d '${pdb_source.pdb.fields.path}.ffdata'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
78 -i '${pdb_source.pdb.fields.path}.ffindex'
1
719931bce361 "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
79 -z '$pdb_source.zipped'
0
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
80 #else
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
81 -d '$pdb_source.ffdata'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
82 -i '$pdb_source.ffindex'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
83 #end if
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
84 </token>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
85 <token name="@hhr_source@">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
86 #if $hhr_source.hhr_source_selector == 'indexed':
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
87 -dh '${hhr_source.hhr.fields.path}.ffdata'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
88 -ih '${hhr_source.hhr.fields.path}.ffindex'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
89 #else
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
90 -dh '$hhr_source.ffdata'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
91 -ih '$hhr_source.ffindex'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
92 #end if
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
93 </token>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
94 </macros>