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comparison quantification.xml @ 1:aba3655fdef0 draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
author watsocam
date Fri, 11 Mar 2022 23:35:52 +0000
parents 928db0f952e3
children 46b897eb2c8e
comparison
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0:928db0f952e3 1:aba3655fdef0
16 16
17 mkdir ./tool_out; 17 mkdir ./tool_out;
18 18
19 @CMD_BEGIN@ 19 @CMD_BEGIN@
20 20
21 python \$QUANT_PATH
21 --masks 22 --masks
22 '${primary_mask.name}'.ome.tiff 23 '${primary_mask.name}'.ome.tiff
23 #if $supp_masks 24 #if $supp_masks
24 #for $mask in $supp_masks: 25 #for $mask in $supp_masks:
25 '${mask.name}'.ome.tiff 26 '${mask.name}'.ome.tiff
26 #end for 27 #end for
27 #end if 28 #end if
28 29
29 --image '${image.name}'.ome.tiff 30 --image '${image.name}'.ome.tiff
30 --output ./tool_out 31 --output ./tool_out
32
33 #if $mask_props
34 --mask_props $mask_props
35 #end if
36 #if $intensity_props
37 --intensity_props $intensity_props
38 #end if
39
31 --channel_names '$channel_names'; 40 --channel_names '$channel_names';
32 41
33 mv ./tool_out/*.csv ./tool_out/quantified.csv; 42 cp tool_out/*cellMasks.csv cellMasks.csv
34 ]]></command> 43 ]]></command>
35 44
36 <inputs> 45 <inputs>
37 <param name="image" type="data" format="tiff" label="Registered TIFF"/> 46 <param name="image" type="data" format="tiff" label="Registered TIFF"/>
38 <param name="primary_mask" type="data" format="tiff" label="Primary Cell Mask"/> 47 <param name="primary_mask" type="data" format="tiff" label="Primary Cell Mask"/>
39 <param name="supp_masks" type="data" multiple="true" optional="true" format="tiff" label="Additional Cell Masks"/> 48 <param name="supp_masks" type="data" multiple="true" optional="true" format="tiff" label="Additional Cell Masks"/>
40 <param name="channel_names" type="data" format="csv" label="Marker Channels"/> 49 <param name="channel_names" type="data" format="csv" label="Marker Channels"/>
50 <param name="mask_props" type="text" label="Mask Metrics" help="Space separated list of additional metrics to be calculated for every mask."/>
51 <param name="intensity_props" type="text" label="Intensity Metrics" help="Space separated list of additional metrics to be calculated for every marker separately."/>
41 </inputs> 52 </inputs>
42 53
43 <outputs> 54 <outputs>
44 <data format="csv" name="quant_out" from_work_dir="./tool_out/quantified.csv" label="${tool.name} on ${on_string}"/> 55 <data format="csv" name="cellmask" from_work_dir="cellMasks.csv" label="CellMaskQuant"/>
45 </outputs> 56 <collection type="list" name="quantification" label="${tool.name} on ${on_string}">
57 <discover_datasets pattern="__designation_and_ext__" format="csv" directory="tool_out/" visible="true"/>
58 </collection>
59 </outputs>
46 <help><![CDATA[ 60 <help><![CDATA[
47 # Single cell quantification 61 # Single cell quantification
48 Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output. 62 Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output.
49 63
50 **CommandSingleCellExtraction.py**: 64 **CommandSingleCellExtraction.py**: