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comparison macros.xml @ 2:187918c47051 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 40737a3341bb2352f4f8560889bb53362fd624be
author goeckslab
date Wed, 28 Dec 2022 19:26:02 +0000
parents 02abff468d60
children c60b810d570d
comparison
equal deleted inserted replaced
1:02abff468d60 2:187918c47051
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <container type="docker">quay.io/goeckslab/mesmer:@TOOL_VERSION@</container> 5 <container type="docker">quay.io/goeckslab/deepcell:@TOOL_VERSION@</container>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <xml name="stdio"> 8 <xml name="stdio">
9 <stdio> 9 <stdio>
10 <regex match="MemoryError" 10 <regex match="MemoryError"
23 source="both" 23 source="both"
24 level="fatal_oom" 24 level="fatal_oom"
25 description="Out of Memory" /> 25 description="Out of Memory" />
26 </stdio> 26 </stdio>
27 </xml> 27 </xml>
28 <xml name="version_cmd"> 28
29 <version_command>@CMD_BEGIN@ --help</version_command> 29 <xml name="watershed_adv_options">
30 <param name="maxima_smooth" type="integer" value="0" label="Maxima Smooth"/>
31 <param name="interior_threshold" type="float" value="0.2" label="Interior Threshold"/>
32 <param name="interior_smooth" type="integer" value="2" label="Interior Smooth"/>
33 <param name="small_objects_threshold" type="integer" value="15" label="Small Objects Threshold"/>
34 <param name="fill_holes_threshold" type="integer" value="15" label="Fill Holes Threshold"/>
35 <param name="radius" type="integer" value="1" label="Radius"/>
30 </xml> 36 </xml>
37
38 <xml name="nuclear_options_macro">
39 <section name="nuclear_options" title="Nuclear Options" expanded="true">
40 <param name="pixel_expansion" type="integer" optional="true" label="Number of pixels to expand nucleus"/>
41 <param name="maxima_threshold" type="float" value="0.1" label="Maxima Threshold"/>
42 <section name="adv_options" title="Advanced Nuclear Options" expanded="false">
43 <expand macro="watershed_adv_options"/>
44 </section>
45 </section>
46 </xml>
47
48 <xml name="wc_options_macro">
49 <section name="wc_options" title="Whole Cell Options" expanded="true">
50 <param name="wc_channels" type="text" value="1" label="The numerical indices of the channel(s) for the membrane markers" help="No quotes, separated by comma. e.g. 0, 1."/>
51 <param name="maxima_threshold" type="float" value="0.075" label="Maxima Threshold"/>
52 <section name="adv_options" title="Advanced Whole Cell Options" expanded="false">
53 <expand macro="watershed_adv_options"/>
54 </section>
55 </section>
56 </xml>
57
31 <xml name="citations"> 58 <xml name="citations">
32 <citations> 59 <citations>
33 <citation type="doi">10.1038/s41587-021-01094-0</citation> 60 <citation type="doi">10.1038/s41587-021-01094-0</citation>
34 </citations> 61 </citations>
35 </xml> 62 </xml>
36 63
37 <token name="@TOOL_VERSION@">0.3.1</token> 64 <token name="@TOOL_VERSION@">0.12.3</token>
38 <token name="@VERSION_SUFFIX@">1</token> 65 <token name="@VERSION_SUFFIX@">2</token>
39 <token name="@CMD_BEGIN@">python /usr/src/app/run_app.py mesmer</token>
40 </macros> 66 </macros>