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comparison coreograph.xml @ 0:99308601eaa6 draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
author perssond
date Wed, 19 May 2021 21:34:38 +0000
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children 57f1260ca94e
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-1:000000000000 0:99308601eaa6
1 <tool id="unet_coreograph" name="UNetCoreograph" version="@VERSION@.3" profile="17.09">
2 <description>Coreograph uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray. It has been trained on 9 TMA slides of different sizes and tissue types.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements"/>
8 @VERSION_CMD@
9
10 <command detect_errors="exit_code"><![CDATA[
11 #set $type_corrected = str($source_image)[:-3]+'ome.tif'
12 ln -s $source_image `basename $type_corrected`;
13
14 @CMD_BEGIN@
15 --imagePath `basename $type_corrected`
16 --downsampleFactor $downsamplefactor
17 --channel $channel
18 --buffer $buffer
19 --sensitivity $sensitivity
20
21 ##if $usegrid
22 ##--useGrid
23 ##end if
24
25 #if $cluster
26 --cluster
27 #end if
28
29 --outputPath .;
30
31 ]]></command>
32
33
34 <inputs>
35 <param name="source_image" type="data" format="tiff" label="Registered TIFF"/>
36 <param name="downsamplefactor" type="integer" value="5" label="Down Sample Factor"/>
37 <param name="channel" type="integer" value="0" label="Channel"/>
38 <param name="buffer" type="float" value="2.0" label="Buffer"/>
39 <param name="sensitivity" type="float" value="0.3" label="Sensitivity"/>
40 <!--<param name="usegrid" type="boolean" label="Use Grid"/>-->
41 <param name="cluster" type="boolean" checked="false" label="Cluster"/>
42 </inputs>
43
44 <outputs>
45 <collection name="tma_sections" type="list" label="${tool.name} on ${on_string}: Images">
46 <discover_datasets pattern="(?P&lt;designation&gt;[0-9]+)\.tif" format="tiff" visible="false"/>
47 </collection>
48 <collection name="masks" type="list" label="${tool.name} on ${on_string}: Masks">
49 <discover_datasets pattern="(?P&lt;designation&gt;[0-9]+)_mask\.tif" directory="masks" format="tiff" visible="false"/>
50 </collection>
51 <data name="TMA_MAP" format="tiff" label="${tool.name} on ${on_string}: TMA Map" from_work_dir="TMA_MAP.tif"/>
52 </outputs>
53 <help><![CDATA[
54 ]]></help>
55 <expand macro="citations" />
56 </tool>