Mercurial > repos > imgteam > 2d_auto_threshold
annotate auto_threshold.xml @ 4:7d80eb2411fb draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
author | imgteam |
---|---|
date | Sat, 07 Jun 2025 18:38:16 +0000 |
parents | 5224cc463a97 |
children |
rev | line source |
---|---|
4
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
1 <tool id="ip_threshold" name="Threshold image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
2 <description>with scikit-image</description> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
3 <macros> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
4 <import>creators.xml</import> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
5 <import>tests.xml</import> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
6 <token name="@TOOL_VERSION@">0.25.0</token> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
7 <token name="@VERSION_SUFFIX@">0</token> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
8 <xml name="inputs/offset"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
9 <param name="offset" type="float" value="0" label="Offset" help="Offset to be added to the automatically determined threshold value. Positive values will increase the threshold (and thus reduce the amount of values above the threshold)." /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
10 </xml> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
11 </macros> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
12 <creator> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
13 <expand macro="creators/bmcv"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
14 </creator> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
15 <edam_operations> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
16 <edam_operation>operation_3443</edam_operation> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
17 </edam_operations> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
18 <xrefs> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
19 <xref type="bio.tools">scikit-image</xref> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
20 <xref type="biii">scikit-image</xref> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
21 </xrefs> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
22 <requirements> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
23 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
24 <requirement type="package" version="0.4.1">giatools</requirement> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
25 </requirements> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
26 <command detect_errors="aggressive"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
27 <![CDATA[ |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
28 |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
29 python '$__tool_directory__/auto_threshold.py' |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
30 |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
31 '$input' |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
32 ./out.tiff |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
33 |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
34 '$th_method.method_id' |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
35 '$th_method.block_size' |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
36 '$th_method.offset' |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
37 '$th_method.threshold1' |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
38 $invert_output |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
39 |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
40 #if str($th_method.threshold2) != '': |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
41 --threshold2 '$th_method.threshold2' |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
42 #end if |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
43 |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
44 ]]> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
45 </command> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
46 <inputs> |
3
5224cc463a97
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
parents:
1
diff
changeset
|
47 <param name="input" type="data" format="tiff,png" label="Input image" /> |
4
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
48 <conditional name="th_method"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
49 <param name="method_id" type="select" label="Thresholding method"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
50 <option value="manual">Manual</option> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
51 <option value="otsu" selected="True">Globally adaptive / Otsu</option> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
52 <option value="li">Globally adaptive / Li's Minimum Cross Entropy</option> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
53 <option value="isodata">Globally adaptive / Isodata</option> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
54 <option value="yen">Globally adaptive / Yen</option> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
55 <option value="loc_gaussian">Locally adaptive / Gaussian</option> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
56 <option value="loc_median">Locally adaptive / Median</option> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
57 <option value="loc_mean">Locally adaptive / Mean</option> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
58 </param> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
59 <when value="manual"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
60 <param name="threshold1" type="float" value="0" label="Threshold value" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
61 <param name="threshold2" type="float" value="" optional="true" label="Second threshold value for hysteresis thresholding" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
62 <param name="block_size" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
63 <param name="offset" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
64 </when> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
65 <when value="otsu"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
66 <param name="threshold1" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
67 <param name="threshold2" type="hidden" value="" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
68 <param name="block_size" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
69 <expand macro="inputs/offset" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
70 </when> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
71 <when value="li"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
72 <param name="threshold1" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
73 <param name="threshold2" type="hidden" value="" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
74 <param name="block_size" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
75 <expand macro="inputs/offset" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
76 </when> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
77 <when value="isodata"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
78 <param name="threshold1" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
79 <param name="threshold2" type="hidden" value="" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
80 <param name="block_size" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
81 <expand macro="inputs/offset" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
82 </when> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
83 <when value="yen"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
84 <param name="threshold1" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
85 <param name="threshold2" type="hidden" value="" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
86 <param name="block_size" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
87 <expand macro="inputs/offset" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
88 </when> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
89 <when value="loc_gaussian"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
90 <param name="threshold1" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
91 <param name="threshold2" type="hidden" value="" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
92 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
93 <expand macro="inputs/offset" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
94 </when> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
95 <when value="loc_median"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
96 <param name="threshold1" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
97 <param name="threshold2" type="hidden" value="" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
98 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
99 <expand macro="inputs/offset" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
100 </when> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
101 <when value="loc_mean"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
102 <param name="threshold1" type="hidden" value="0" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
103 <param name="threshold2" type="hidden" value="" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
104 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
105 <expand macro="inputs/offset" /> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
106 </when> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
107 </conditional> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
108 <param name="invert_output" type="boolean" checked="false" truevalue="--invert_output" falsevalue="" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." /> |
0
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
109 </inputs> |
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
110 <outputs> |
4
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
111 <data format="tiff" name="output" from_work_dir="out.tiff" /> |
0
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
112 </outputs> |
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
113 <tests> |
4
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
114 <!-- Tests for single-channel images (TIFF) --> |
0
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
115 <test> |
4
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
116 <param name="input" value="sample.tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
117 <conditional name="th_method"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
118 <param name="method_id" value="loc_gaussian"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
119 <param name="block_size" value="51"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
120 </conditional> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
121 <expand macro="tests/binary_image_diff" name="output" value="out1.tiff" ftype="tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
122 </test> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
123 <test> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
124 <param name="input" value="sample.tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
125 <conditional name="th_method"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
126 <param name="method_id" value="loc_gaussian"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
127 <param name="block_size" value="51"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
128 <param name="offset" value="1"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
129 </conditional> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
130 <expand macro="tests/binary_image_diff" name="output" value="out2.tiff" ftype="tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
131 </test> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
132 <test> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
133 <param name="input" value="sample.tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
134 <conditional name="th_method"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
135 <param name="method_id" value="otsu"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
136 </conditional> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
137 <expand macro="tests/binary_image_diff" name="output" value="out3.tiff" ftype="tiff"/> |
0
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
138 </test> |
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
139 <test> |
4
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
140 <param name="input" value="sample.tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
141 <param name="invert_output" value="True"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
142 <conditional name="th_method"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
143 <param name="method_id" value="manual"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
144 <param name="threshold1" value="64"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
145 </conditional> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
146 <expand macro="tests/binary_image_diff" name="output" value="out4.tiff" ftype="tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
147 </test> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
148 <test> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
149 <param name="input" value="sample.tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
150 <conditional name="th_method"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
151 <param name="method_id" value="manual"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
152 <param name="threshold1" value="180"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
153 <param name="threshold2" value="240"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
154 </conditional> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
155 <expand macro="tests/binary_image_diff" name="output" value="sample_manual_180_240.tiff" ftype="tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
156 </test> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
157 <!-- Tests for multi-channel images (PNG) --> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
158 <test> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
159 <param name="input" value="rgb.png"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
160 <conditional name="th_method"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
161 <param name="method_id" value="otsu"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
162 </conditional> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
163 <expand macro="tests/binary_image_diff" name="output" value="rgb_otsu.tiff" ftype="tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
164 </test> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
165 <!-- Tests for irregular files --> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
166 <test> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
167 <param name="input" value="sample2.tiff"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
168 <conditional name="th_method"> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
169 <param name="method_id" value="otsu"/> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
170 </conditional> |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
171 <expand macro="tests/binary_image_diff" name="output" value="out5.tiff" ftype="tiff"/> |
0
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
172 </test> |
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
173 </tests> |
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
174 <help> |
4
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
175 |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
176 **Applies a standard thresholding algorithm to a 2-D single-channel image. Yields a binary image.** |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
177 |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
178 The thresholding algorithm automatically determines a threshold value (unless manual thresholding is used). |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
179 The input image is then thresholded, by assigning white (pixel value 255) to image regions above the determined threshold, |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
180 and black (pixel value 0) to image regions below or equal to the determined threshold. |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
181 |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
182 The assignment of black and white to image regions below and above the threshold is inverted, if the corresponding option is set. |
7d80eb2411fb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents:
3
diff
changeset
|
183 |
0
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
184 </help> |
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
185 <citations> |
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
186 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
187 </citations> |
6fc65082d1e6
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff
changeset
|
188 </tool> |