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comparison coreograph.xml @ 1:57f1260ca94e draft

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"planemo upload commit fec9dc76b3dd17b14b02c2f04be9d30f71eba1ae"
author watsocam
date Fri, 11 Mar 2022 23:40:51 +0000
parents 99308601eaa6
children 224e0cf4aaeb
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0:99308601eaa6 1:57f1260ca94e
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #set $type_corrected = str($source_image)[:-3]+'ome.tif' 11 #set $type_corrected = str($source_image)[:-3]+'ome.tif'
12 ln -s $source_image `basename $type_corrected`; 12 ln -s $source_image `basename $type_corrected`;
13 13
14 @CMD_BEGIN@ 14 @CMD_BEGIN@
15
16 python \$UNET_PATH
15 --imagePath `basename $type_corrected` 17 --imagePath `basename $type_corrected`
16 --downsampleFactor $downsamplefactor 18 --downsampleFactor $downsamplefactor
17 --channel $channel 19 --channel $channel
18 --buffer $buffer 20 --buffer $buffer
19 --sensitivity $sensitivity 21 --sensitivity $sensitivity
22 ##--useGrid 24 ##--useGrid
23 ##end if 25 ##end if
24 26
25 #if $cluster 27 #if $cluster
26 --cluster 28 --cluster
29 #end if
30
31 #if $tissue
32 --tissue
27 #end if 33 #end if
28 34
29 --outputPath .; 35 --outputPath .;
30 36
31 ]]></command> 37 ]]></command>
37 <param name="channel" type="integer" value="0" label="Channel"/> 43 <param name="channel" type="integer" value="0" label="Channel"/>
38 <param name="buffer" type="float" value="2.0" label="Buffer"/> 44 <param name="buffer" type="float" value="2.0" label="Buffer"/>
39 <param name="sensitivity" type="float" value="0.3" label="Sensitivity"/> 45 <param name="sensitivity" type="float" value="0.3" label="Sensitivity"/>
40 <!--<param name="usegrid" type="boolean" label="Use Grid"/>--> 46 <!--<param name="usegrid" type="boolean" label="Use Grid"/>-->
41 <param name="cluster" type="boolean" checked="false" label="Cluster"/> 47 <param name="cluster" type="boolean" checked="false" label="Cluster"/>
48 <param name="tissue" type="boolean" checked="false" label="Tissue"/>
42 </inputs> 49 </inputs>
43 50
44 <outputs> 51 <outputs>
45 <collection name="tma_sections" type="list" label="${tool.name} on ${on_string}: Images"> 52 <collection name="tma_sections" type="list" label="${tool.name} on ${on_string}: Images">
46 <discover_datasets pattern="(?P&lt;designation&gt;[0-9]+)\.tif" format="tiff" visible="false"/> 53 <discover_datasets pattern="(?P&lt;designation&gt;[0-9]+)\.tif" format="tiff" visible="false"/>