annotate macros.xml @ 2:cfcfe731de55 draft default tip

"planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
author guerler
date Thu, 08 Apr 2021 18:22:14 +0000
parents e56e0f4c84fb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
1 <macros>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
2 <xml name="requirements">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
3 <requirements>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
4 <requirement type="package" version="@TOOL_VERSION@">springsuite</requirement>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
5 <yield />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
6 </requirements>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
7 </xml>
1
e56e0f4c84fb "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
8 <token name="@TOOL_VERSION@">0.2</token>
0
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
9 <token name="@VERSION_SUFFIX@">0</token>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
10
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
11 <xml name="ffindex_single_inputs">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
12 <param name="ffdata" type="data" format="ffdata" label="PDB Database" help="Database Data file." />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
13 <param name="ffindex" type="data" format="ffindex" label="PDB Database Index" help="Database Index file." />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
14 </xml>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
15
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
16 <xml name="ffindex_single_inputs_hhr">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
17 <param name="ffdata" type="data" format="ffdata" label="HHR Database" help="Database Data file." />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
18 <param name="ffindex" type="data" format="ffindex" label="HHR Database Index" help="Database Index file." />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
19 </xml>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
20
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
21 <xml name="citations">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
22 <citations>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
23 <citation type="doi">10.1021/ci300579r</citation>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
24 </citations>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
25 </xml>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
26 <xml name="logfile">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
27 <param name="logfile" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log file" />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
28 </xml>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
29
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
30 <xml name="pdb_source">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
31 <conditional name="pdb_source">
64cb5fab9c60 "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">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
33 <option value="indexed" selected="true">Use a built-in index</option>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
34 <option value="history">Use a PDB index from history</option>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
35 </param>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
36 <when value="indexed">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
37 <param name="pdb" type="select" label="Select PDB database" help="">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
38 <options from_data_table="ffindex_indices">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
39 <filter type="sort_by" column="0" />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
40 <filter type="static_value" column="3" value="pdb" />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
41 <validator type="no_options" message="No indices are available" />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
42 </options>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
43 </param>
1
e56e0f4c84fb "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
44 <param name="zipped" type="select" label="Zipped entries in PDB database?" help="">
e56e0f4c84fb "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
45 <option value="" selected="true">No</option>
e56e0f4c84fb "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
46 <option value="gz">Yes</option>
e56e0f4c84fb "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
47 </param>
0
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
48 </when>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
49 <when value="history">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
50 <expand macro="ffindex_single_inputs" />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
51 </when>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
52 </conditional>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
53 </xml>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
54 <xml name="hhr_source">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
55 <conditional name="hhr_source">
64cb5fab9c60 "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">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
57 <option value="indexed" selected="true">Use a built-in index</option>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
58 <option value="history">Use a HHR index from history</option>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
59 </param>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
60 <when value="indexed">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
61 <param name="hhr" type="select" label="Select HHR database" help="">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
62 <options from_data_table="ffindex_indices">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
63 <filter type="sort_by" column="0" />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
64 <filter type="static_value" column="3" value="hhr" />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
65 <validator type="no_options" message="No indices are available" />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
66 </options>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
67 </param>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
68 </when>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
69 <when value="history">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
70 <expand macro="ffindex_single_inputs_hhr" />
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
71 </when>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
72 </conditional>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
73 </xml>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
74
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
75 <token name="@pdb_source@">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
76 #if $pdb_source.pdb_source_selector == 'indexed':
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
77 -d '${pdb_source.pdb.fields.path}.ffdata'
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
78 -i '${pdb_source.pdb.fields.path}.ffindex'
1
e56e0f4c84fb "planemo upload commit aa6c4b1d15a2d5361d68c7eb313551bddf2700fa"
guerler
parents: 0
diff changeset
79 -z '$pdb_source.zipped'
0
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
80 #else
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
81 -d '$pdb_source.ffdata'
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
82 -i '$pdb_source.ffindex'
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
83 #end if
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
84 </token>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
85 <token name="@hhr_source@">
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
86 #if $hhr_source.hhr_source_selector == 'indexed':
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
87 -dh '${hhr_source.hhr.fields.path}.ffdata'
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
88 -ih '${hhr_source.hhr.fields.path}.ffindex'
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
89 #else
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
90 -dh '$hhr_source.ffdata'
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
91 -ih '$hhr_source.ffindex'
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
92 #end if
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
93 </token>
64cb5fab9c60 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
94 </macros>