Mercurial > repos > ximgchess > hexrd

annotate macros.xml @ 8:4bb02acaaabc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 15bca193042c05f262db5cb1efe70e2cbd567615-dirty"
author ximgchess
date Thu, 20 Jan 2022 17:56:47 +0000
parents baba452d0613
children e67ad9795525
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
1 <macros>
8
4bb02acaaabc "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 15bca193042c05f262db5cb1efe70e2cbd567615-dirty"
ximgchess
parents: 7
diff changeset
2 <token name="@TOOL_VERSION@">0.8.17</token>
4bb02acaaabc "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 15bca193042c05f262db5cb1efe70e2cbd567615-dirty"
ximgchess
parents: 7
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
6
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
4 <token name="@PROFILE@">21.09</token>
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
5 <xml name="requirements">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
6 <requirements>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
8 <yield/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
9 </requirements>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
10 </xml>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
11 <xml name="citations">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
12 <citations>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
13 <citation type="doi">10.1016/j.matchar.2020.110366</citation>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
14 <yield />
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
15 </citations>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
16 </xml>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
17
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
18 <token name="@CMD_IMPORTS@">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
19 #import re
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
20 #import yaml
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
21
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
22 #set global $img_panel_dict = dict()
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
23 #if $detector.panel_assignment == 'panel_table'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
24 #set $fh = open(str($detector.image_panel_table),'r')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
25 #for $line in $fh:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
26 #set $fields = $line.strip().split('\t')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
27 #silent $img_panel_dict[$fields[0]] = $fields[1]
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
28 #end for
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
29 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
30 #set global $panels = $yaml.safe_load(open(str($instrument),'r'))['detectors'].keys()
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
31 #def identifier_or_name($input1)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
32 #if hasattr($input1, 'element_identifier')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
33 #return $input1.element_identifier
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
34 #elif hasattr($input1, 'name')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
35 #return $input1.name
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
36 #else
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
37 #return str($input1)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
38 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
39 #end def
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
40 #def clean($name1)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
41 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](npz|hexrd|yml|dat|out)$','', $name1.split()[-1]))
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
42 #return $name_clean
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
43 #end def
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
44 #def ln_name($ds,$ext)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
45 #set $lname = "%s.%s" % ($clean($identifier_or_name($ds)),$ext)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
46 #return $lname
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
47 #end def
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
48 #def get_panel($img_input):
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
49 #set $img_name = $identifier_or_name($img_input)
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
50 #if $img_panel_dict and $img_name in $img_panel_dict:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
51 #return $img_panel_dict[$img_name]
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
52 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
53 #for $p in $panels:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
54 #if $p in $img_name:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
55 #return $p
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
56 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
57 #end for
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
58 #return $img_name
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
59 #end def
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
60 </token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
61
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
62 <xml name="common_config" token_multiple_inputs="true" >
6
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
63 <param name="inputs" type="data" format="hexrd.images.npz" multiple="true" label="Image series frame-cache"/>
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
64 <conditional name="detector">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
65 <param name="panel_assignment" type="select" label="Assign detector panel to images">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
66 <option value="infer_from_name" selected="true">Infer the panel from the image name</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
67 <option value="panel_table">Input a table with image panels assignments</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
68 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
69 <when value="infer_from_name"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
70 <when value="panel_table">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
71 <param name="image_panel_table" type="data" format="tabular" label="Image panel assignment table">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
72 <help>A 2-column table:image dataset name detector panel name</help>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
73 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
74 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
75 </conditional>
7
baba452d0613 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c6c9ce811a27cdee735c2eeac9f6a29f95d9ae90"
ximgchess
parents: 6
diff changeset
76 <param name="instrument" type="data" format="yaml" label="instrument"/>
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
77 <param name="material" type="data" format="hexrd.materials.h5" label="material"/>
6
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
78 <param name="active_material" type="select" label="active material name">
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
79 <options>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
80 <filter type="data_meta" ref="material" key="materials"/>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
81 </options>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
82 </param>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
83 <param name="dmin" type="float" value="1.0" min="0" max="10" optional="true" label="dmin angstroms" help="used to figure out the maximum sampling for g-vectors default 1.0"/>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
84 <param name="tth_width" type="float" value="0.25" min="0" max="10" optional="true" label="tth tolerance in degrees" help="tth_width default 0.25 "/>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
85 <param name="min_sfac_ratio" type="float" value="" min="0" max="1" optional="true" label="min percentage of max to exclude" help="min_sfac_ratio min percentage of max |F|^2 to exclude; default None"/>
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
86 <!--
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
87 <param name="active_material" type="text" value="" label="active material name">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
88 <validator type="empty_field" />
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
89 </param>
6
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
90 -->
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
91 </xml>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
92
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
93 <token name="@CMD_LINKS@"><![CDATA[@CMD_IMPORTS@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
94 mkdir -p imageseries &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
95 ln -s '$material' $ln_name($material,'h5') &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
96 ln -s '$instrument' $ln_name($instrument,'yml') &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
97 #for $input in $inputs
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
98 ln -s '$input' imageseries/$ln_name($input,'npz') &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
99 #end for
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
100 ]]>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
101 </token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
102 <token name="@FIT_GRAIN_LINKS@"><![CDATA[@CMD_LINKS@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
103 ln -s '$ome_map' $ln_name($ome_map,'npz') &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
104 ln -s '$accepted_orientations' $ln_name($accepted_orientations,'dat') &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
105 ##mkdir -p analysis &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
106 ##cp '$grains_estimate' analysis/$ln_name($grains_estimate,'out') &&
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
107 ]]>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
108 </token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
109
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
110 <token name="@CONVERT2TAB@"><![CDATA[for i in `find analysis -name '[gs]*.out'`; do sed -i.bak "s/[ ][ ][ ]*/\$(printf '\t')/g" \${i}; done]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
111
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
112 <token name="@COMMON_YML@"><![CDATA[@CMD_IMPORTS@
6
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
113 #slurp
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
114 #set instrument_file = $ln_name($instrument,'yml')
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
115 analysis_name: analysis
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
116
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
117 multiprocessing: -1
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
118
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
119 material:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
120 definitions: $ln_name($material,'h5')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
121 active: $active_material
6
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
122 #if $dmin
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
123 dmin: $dmin # defaults to 1.0 angstrom
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
124 #end if
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
125 #if $tth_width
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
126 tth_width: $tth_width # defaults to 0.25 degrees
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
127 #end if
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
128 #if $min_sfac_ratio
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
129 min_sfac_ratio: $min_sfac_ratio # min percentage of max |F|^2 to exclude; default None
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
130 #end if
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
131
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
132 image_series:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
133 format: frame-cache
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
134 data:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
135 #for $input in $inputs
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
136 - file: imageseries/$ln_name($input,'npz')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
137 args: {}
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
138 panel: $get_panel($input) # must match detector key
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
139 #end for
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
140
6
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
141 instrument: $instrument_file
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
142
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
143 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
144
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
145 <xml name="find_orientations_config">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
146 <expand macro="common_config" token_multiple_inputs="true" />
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
147 <section name="orientation_maps" title="Orientation Maps" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
148 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
149 <param name="bin_frames" type="integer" value="1" label="bin frames"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
150 <!-- active_hkls should be able to be optional="true" -->
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
151 <param name="active_hkls" type="text" value="" label="active hkl planes">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
152 <help>commas separated list of planes, e.g.: 0,1,2,3,4,5</help>
8
4bb02acaaabc "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 15bca193042c05f262db5cb1efe70e2cbd567615-dirty"
ximgchess
parents: 7
diff changeset
153 <validator type="regex" message="plane indices separated by commas">^\d(,\d)*$</validator>
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
154 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
155 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
156 <param name="on_map_threshold" type="integer" value="1" min="1" label="on-map threshold used in the scoring"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
157 <section name="search_options" title="Search Options" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
158 <conditional name="search">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
159 <param name="search_type" type="select" label="Specify Search">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
160 <option value="seed_search" selected="true">use seed search</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
161 <option value="use_quaternion_grid">use quaternion grid</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
162 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
163 <when value="seed_search">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
164 <!-- hkl_seeds should be able to be optional="true" -->
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
165 <param name="hkl_seeds" type="text" value="" label="hkl seeds">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
166 <help>commas separated list of planes, e.g.: 0,1,2 (subset of active hkl planes)</help>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
167 <validator type="regex" message="">^\d(,\d)*$</validator>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
168 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
169 <param name="fiber_step" type="float" value="0.5" min="0" max="10" label="fiber step"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
170 <conditional name="params">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
171 <param name="method" type="select" label="Method">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
172 <option value="label" selected="true">label</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
173 <option value="blob_dog">blob_dog</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
174 <option value="blob_log">blob_log</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
175 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
176 <when value="label">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
177 <param name="filter_radius" type="integer" value="1" min="1" label="label filter radius"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
178 <param name="threshold" type="integer" value="1" min="1" label="label threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
179 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
180 <when value="blob_dog">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
181 <param name="min_sigma" type="float" value="0.5" min="0" max="10" label="blob_dog min_sigma"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
182 <param name="max_sigma" type="float" value="5.0" min="0" max="10" label="blob_dog max_sigma"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
183 <param name="sigma_ratio" type="float" value="1.6" min="0" max="10" label="blob_dog sigma_ratio"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
184 <param name="threshold" type="float" value="0.01" min="0" max="1.0" label="blob_dog threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
185 <param name="overlap" type="float" value="0.1" min="0" max="1.0" label="blob_dog overlap"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
186 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
187 <when value="blob_log">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
188 <param name="min_sigma" type="float" value="0.5" min="0" max="10" label="blob_log min_sigma"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
189 <param name="max_sigma" type="float" value="5.0" min="0" max="10" label="blob_log max_sigma"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
190 <param name="num_sigma" type="integer" value="10" min="0" max="20" label="blob_log num_sigma"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
191 <param name="threshold" type="float" value="0.01" min="0" max="1.0" label="blob_log threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
192 <param name="overlap" type="float" value="0.1" min="0" max="1.0" label="blob_log overlap"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
193 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
194 </conditional>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
195 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
196 <when value="use_quaternion_grid">
7
baba452d0613 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c6c9ce811a27cdee735c2eeac9f6a29f95d9ae90"
ximgchess
parents: 6
diff changeset
197 <param name="quaternion_grid" type="data" format="npz" label="quaterion grid file"/>
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
198 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
199 </conditional>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
200 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
201 <section name="omega" title="Omega" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
202 <param name="omega_tolerance" type="float" value="1.0" min="0" max="10.0" label="omega tolerance"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
203 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
204 <section name="eta" title="eta" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
205 <param name="eta_tolerance" type="float" value="1.0" min="0" max="10.0" label="eta tolerance"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
206 <param name="eta_mask" type="float" value="5.0" min="0" max="10.0" label="eta mask"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
207 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
208 <section name="clustering" title="Clustering" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
209 <param name="clustering_algorithm" type="select" label="Clustering algorithm">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
210 <option value="dbscan" selected="true">dbscan</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
211 <option value="sph-dbscan">sph-dbscan</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
212 <option value="ort-dbscan">ort-dbscan</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
213 <option value="fclusterdata">fclusterdata (won't work for large problems)</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
214 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
215 <param name="clustering_radius" type="float" value="1.0" min="0" max="10" label="clustering radius"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
216 <param name="clustering_completeness" type="float" value="0.85" min="0" max="1" label="clustering completeness threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
217 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
218 <!--
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
219 -->
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
220 </xml>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
221
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
222 <token name="@FIND_ORIENTATIONS_YML@"><![CDATA[@COMMON_YML@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
223
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
224 #set active_hkls = 'all'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
225 #if $orientation_maps.active_hkls:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
226 #set active_hkls = '[' + str($orientation_maps.active_hkls) + ']'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
227 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
228 find_orientations:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
229 orientation_maps:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
230 # A file name must be specified. If it doesn't exist, one will be created
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
231 file: null
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
232
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
233 threshold: $orientation_maps.threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
234 bin_frames: $orientation_maps.bin_frames # defaults to 1
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
235
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
236 # "all", or a list of hkl orders used to find orientations
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
237 # defaults to all orders listed in the material definition
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
238 active_hkls: $active_hkls
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
239
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
240 # either search full quaternion grid, or seed search based on sparse
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
241 # orientation maps. For input search space:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
242 #
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
243 # use_quaternion_grid: some/file/name
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
244 #
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
245 # otherwise defaults to seeded search
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
246 #if $search_options.search.search_type == 'use_quaternion_grid'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
247 use_quaternion_grid:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
248 #elif $search_options.search.search_type == 'seed_search'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
249 #set hkl_seeds = '[' + str($search_options.search.hkl_seeds) + ']'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
250 seed_search: # this section is ignored if use_quaternion_grid is defined
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
251 hkl_seeds: $hkl_seeds # hkls ids to use, must be defined for seeded search
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
252 fiber_step: $search_options.search.fiber_step # degrees, defaults to ome tolerance
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
253 # Method selection:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
254 # Now 3 choices: label (the original), 'blob_dog', and 'blob_log'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
255 # Each has its own parameter names, examples below.
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
256 #
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
257 method:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
258 #if $search_options.search.params.method == 'label'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
259 label:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
260 filter_radius: $search_options.search.params.filter_radius
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
261 threshold: $search_options.search.params.threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
262 #elif $search_options.search.params.method == 'blob_dog'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
263 blob_dog:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
264 min_sigma: $search_options.search.params.min_sigma
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
265 max_sigma: $search_options.search.params.max_sigma
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
266 sigma_ratio: $search_options.search.params.sigma_ratio
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
267 threshold: $search_options.search.params.threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
268 overlap: $search_options.search.params.overlap
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
269 #elif $search_options.search.params.method == 'blob_log'
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
270 blob_log:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
271 min_sigma: $search_options.search.params.min_sigma
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
272 max_sigma: $search_options.search.params.max_sigma
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
273 num_sigma: $search_options.search.params.num_sigma
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
274 threshold: $search_options.search.params.threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
275 overlap: $search_options.search.params.overlap
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
276 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
277 # this is the on-map threshold using in the scoring
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
278 # defaults to 1
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
279 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
280 threshold: $on_map_threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
281
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
282 omega:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
283 tolerance: $omega.omega_tolerance # in degrees, defaults to 2x ome step
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
284
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
285 eta:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
286 tolerance: $eta.eta_tolerance # in degrees, defaults to 2x ome step
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
287 mask: $eta.eta_mask # degrees, mask angles close to ome rotation axis, defaults to 5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
288
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
289 clustering:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
290 # algorithm choices are
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
291 # sph-dbscan
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
292 # ort-dbscn
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
293 # dbscan <default>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
294 # fclusterdata; this is a fallback and won't work for large problems
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
295 algorithm: $clustering.clustering_algorithm
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
296 radius: $clustering.clustering_radius
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
297 completeness: $clustering.clustering_completeness
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
298
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
299 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
300
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
301 <xml name="fit_grains_config">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
302 <expand macro="common_config" token_multiple_inputs="true"/>
6
164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
ximgchess
parents: 5
diff changeset
303 <param name="ome_map" type="data" format="hexrd.eta_ome.npz" label="analysis eta-ome_maps.npz from find_orientations"/>
7
baba452d0613 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c6c9ce811a27cdee735c2eeac9f6a29f95d9ae90"
ximgchess
parents: 6
diff changeset
304 <param name="accepted_orientations" type="data" format="tabular" label="accepted_orientations from find_orientations"/>
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
305 <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
306 <param name="do_fit" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fit grains" help="if false, extracts grains but doesn't fit"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
307 <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
308 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
309 <section name="tolerance" title="Fit Grain Tolerance" expanded="true">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
310 <repeat name="tolerance_lists" title="Tolerance values" min="1">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
311 <param name="tth" type="float" value="" min="0" label="tth"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
312 <param name="eta" type="float" value="" min="0" label="eta"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
313 <param name="omega" type="float" value="" min="0" label="omega"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
314 </repeat>
8
4bb02acaaabc "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 15bca193042c05f262db5cb1efe70e2cbd567615-dirty"
ximgchess
parents: 7
diff changeset
315 <param name="refit" type="text" value="1" label="refit" help="float values separated by commas">
4bb02acaaabc "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 15bca193042c05f262db5cb1efe70e2cbd567615-dirty"
ximgchess
parents: 7
diff changeset
316 <validator type="regex" message="">^[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?(,[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?)*$</validator>
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
317 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
318 <conditional name="max_tth">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
319 <param name="tth_max_value" type="select" label="Set tth_max">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
320 <option value="true" selected="true">true</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
321 <option value="false">false</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
322 <option value="entered">enter value</option>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
323 </param>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
324 <when value="true"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
325 <when value="false"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
326 <when value="entered">
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
327 <param name="tth_max" type="float" value="14.25" label="tth_max"/>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
328 </when>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
329 </conditional>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
330 </section>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
331 </xml>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
332
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
333 <token name="@FIT_GRAINS_YML@"><![CDATA[@COMMON_YML@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
334 find_orientations:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
335 orientation_maps:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
336 # A file name must be specified. If it doesn't exist, one will be created
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
337 file: $ln_name($ome_map,'npz')
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
338
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
339 fit_grains:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
340 do_fit: $do_fit # if false, extracts grains but doesn't fit. defaults to true
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
341 # estimate: null
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
342 npdiv: $npdiv # number of polar pixel grid subdivisions, defaults to 2
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
343 threshold: $threshold
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
344
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
345 #set $tth = []
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
346 #set $eta = []
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
347 #set $omega = []
8
4bb02acaaabc "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 15bca193042c05f262db5cb1efe70e2cbd567615-dirty"
ximgchess
parents: 7
diff changeset
348 #set $refit = '[' + str($tolerance.refit) + ']'
5
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
349 #for $tol in $tolerance.tolerance_lists
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
350 #silent $tth.append(float($tol.tth))
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
351 #silent $eta.append(float($tol.eta))
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
352 #silent $omega.append(float($tol.omega))
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
353 #end for
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
354 tolerance:
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
355 tth: $tth # tolerance lists must be identical length
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
356 eta: $eta
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
357 omega: $omega
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
358
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
359 refit: $refit
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
360 #if $tolerance.max_tth.tth_max_value == 'entered':
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
361 tth_max: $tolerance.max_tth.tth_max # true, false, or a non-negative value, defaults to true
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
362 #else
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
363 tth_max: $tolerance.max_tth.tth_max_value # true, false, or a non-negative value, defaults to true
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
364 #end if
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
365 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
366 <token name="@HEXRD_HELP@"><![CDATA[
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
367 HEXRD_ provides analysis of x-ray diffraction data, especially high-energy x-ray diffraction. HEXRD is comprised of a library and API for writing scripts, a command line interface, and an interactive graphical user interface.
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
368
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
369 .. _HEXRD: https://github.com/HEXRD/hexrd
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
370 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
371
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
372 <token name="@COMMON_INPUTS_HELP@"><![CDATA[
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
373
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
374 **INPUTS**
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
375
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
376 - imageseries - Detector image files converted to sparse matrix compressed numpy arrays.
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
377 - instrument - A yaml file that decribes the instrument
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
378 - materials.hexrd - A "pickled" hexrd Materials object that desscribes the sample material
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
379 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
380 <token name="@FIT_GRAIN_INPUTS_HELP@"><![CDATA[@COMMON_INPUTS_HELP@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
381 - analysis eta-ome_maps.npz from find_orientations
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
382 - accepted_orientations from find_orientations
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
383
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
384 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
385
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
386 <token name="@COMMON_OUTPUTS_HELP@"><![CDATA[
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
387
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
388 **OUTPUTS**
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
389
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
390 - config yaml - parameter for hexrd
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
391 - log - the hexrd logging output
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
392 - grains.out
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
393 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
394 <token name="@FIND_ORIENTATIONS_OUTPUTS_HELP@"><![CDATA[@COMMON_OUTPUTS_HELP@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
395 - analysis eta-ome_maps.npz *(used as input for hexrd fit-grains)*
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
396 - analysis accepted_orientations_analysis.dat *(used as input for hexrd fit-grains)*
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
397 - analysis scored_orientations_analysis.npz
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
398 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
399 <token name="@FIT_GRAINS_OUTPUTS_HELP@"><![CDATA[@COMMON_OUTPUTS_HELP@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
400 - Collection of spots.out
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
401 ]]></token>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
402
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
403
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
404 </macros>