Mercurial > repos > perssond > unmicst

annotate unmicst.xml @ 1:74fe58ff55a5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
author goeckslab
date Wed, 07 Sep 2022 23:10:14 +0000
parents 6bec4fef6b2e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
1 <tool id="unmicst" name="UnMicst" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
2 <description>Image segmentation - probability map generation</description>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
3
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
4 <macros>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
5 <import>macros.xml</import>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
6 </macros>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
7
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
8 <expand macro="requirements"/>
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
9 <expand macro="version_cmd"/>
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
10
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
12 #set $ext = str($image.file_ext)
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
13 #if $ext == 'tiff'
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
14 #set $ext = 'tif'
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
15 #end if
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
16 #set $input = 'image.' + str($ext)
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
17
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
18 ln -s '$image' '$input' &&
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
19
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
20 @CMD_BEGIN@ '$input'
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
21
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
22 --tool $tool
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
23
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
24 #if $stackoutput
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
25 --stackOutput
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
26 #end if
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
27
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
28 --outputPath '.'
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
29 --channel $channel
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
30 --model $model
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
31 --mean $mean
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
32 --std $stdev
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
33 --scalingFactor $scalingfactor
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
34 --outlier $outlier &&
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
35
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
36 ## Move files to different files for from_work_dir differentiation
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
37 #if $stackoutput
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
38 mv *Probabilities*.tif Probabilities.tif &&
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
39 mv qc/*Preview*.tif Preview.tif
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
40 #else
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
41 mv *ContoursPM*.tif ContoursPM.tif &&
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
42 mv *NucleiPM*.tif NucleiPM.tif
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
43 #end if
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
44 ]]></command>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
45
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
46 <inputs>
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
47 <param name="tool" type="select" label="UnMicst Tool">
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
48 <option selected="true" value="unmicst-solo">unmicst-solo</option>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
49 <option value="unmicst-duo">unmicst-duo</option>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
50 <option value="unmicst-legacy">unmicst-legacy</option>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
51 <option value="UnMicstCyto2">UnMicstCyto2</option>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
52 </param>
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
53 <param name="image" type="data" format="tiff" label="Registered TIFF"/>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
54 <param name="model" type="select" label="Model">
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
55 <option value="nucleiDAPI">nucleiDAPI</option>
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
56 <option value="CytoplasmIncell">CytoplasmIncell</option>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
57 <option value="CytoplasmIncell2">CytoplasmIncell2</option>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
58 <option value="CytoplasmZeissNikon">CytoplasmZeissNikon</option>
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
59 <option value="mousenucleiDAPI">mousenucleiDAPI</option>
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
60 <option value="nucleiDAPI1-5">nucleiDAPI1-5</option>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
61 <option value="nucleiDAPILAMIN">nucleiDAPILAMIN</option>
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
62 </param>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
63 <param name="mean" type="float" value="-1" label="Mean (-1 for model default)"/>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
64 <param name="stdev" type="float" value="-1" label="Standard Deviation (-1 for model default)"/>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
65 <param name="channel" type="integer" value="0" label="Channel to perform inference on"/>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
66 <param name="stackoutput" type="boolean" label="Stack probability map outputs"/>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
67 <param name="scalingfactor" type="float" value="1.0" label="Factor to scale by"/>
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
68 <param name="outlier" type="float" value="-1.0" label="Map percentile intensity to max when rescaling intensity values"/>
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
69 </inputs>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
70
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
71 <outputs>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
72 <data format="tiff" name="previews" from_work_dir="Preview.tif" label="${tool.name} on ${on_string}: Preview">
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
73 <filter>stackoutput</filter>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
74 </data>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
75 <data format="tiff" name="probabilities" from_work_dir="Probabilities.tif" label="${tool.name} on ${on_string}: Probabilities">
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
76 <filter>stackoutput</filter>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
77 </data>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
78 <data format="tiff" name="contours" from_work_dir="ContoursPM.tif" label="${tool.name} on ${on_string}: ContoursPM">
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
79 <filter>not stackoutput</filter>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
80 </data>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
81 <data format="tiff" name="nuclei" from_work_dir="NucleiPM.tif" label="${tool.name} on ${on_string}: NucleiPM">
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
82 <filter>not stackoutput</filter>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
83 </data>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
84 </outputs>
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
85 <tests>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
86 <test expect_num_outputs="2">
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
87 <param name="image" value="105.tif" ftype="tiff" />
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
88 <param name="model" value="nucleiDAPI" />
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
89 <param name="tool" value="unmicst-legacy"/>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
90 <param name="channel" value="1"/>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
91 <output name="nuclei" file="105_NucleiPM_1.tif" compare="sim_size" delta="10" />
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
92 <output name="contours" file="105_ContoursPM_1.tif" compare="sim_size" delta="10" />
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
93 </test>
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
94 </tests>
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
95 <help><![CDATA[
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
96 -------
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
97 UNMICST
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
98 -------
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
99
1
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
100 **UnMICST** uses a convolutional neural network to annotate each pixel with the probability that it belongs to a given subcellular component (nucleus, cytoplasm, cell boundary). Check the UnMICST website for the most up-to-date documentation.
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
101 **Input**
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
102 An .ome.tif, preferably flat field corrected. The model is trained on images acquired at a pixelsize of 0.65 microns/px. If your settings differ, you can upsample/downsample to some extent.
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
103 **Output**
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
104 1. a .tif stack where the different probability maps for each class are concatenated in the Z-axis in the order: nuclei foreground, nuclei contours, and background.
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
105 2. a QC image with the DNA image concatenated with the nuclei contour probability map with suffix Preview
74fe58ff55a5 planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
goeckslab
parents: 0
diff changeset
106 More infortion available at: https://labsyspharm.github.io/UnMICST-info/.
0
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
107 ]]></help>
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
108 <expand macro="citations" />
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff changeset
109 </tool>