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comparison quantification.xml @ 2:46b897eb2c8e draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"
author watsocam
date Wed, 30 Mar 2022 16:56:29 +0000
parents aba3655fdef0
children c09e444635d9
comparison
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1:aba3655fdef0 2:46b897eb2c8e
1 <tool id="quantification" name="Quantification" version="@VERSION@.5" profile="17.09"> 1 <tool id="quantification" name="Quantification" version="@VERSION@.6" profile="17.09">
2 <description>Single cell quantification, a module for single-cell data extraction given a segmentation mask and multi-channel image.</description> 2 <description>Single cell quantification, a module for single-cell data extraction given a segmentation mask and multi-channel image.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 6
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 @VERSION_CMD@ 8 @VERSION_CMD@
9 9
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 ln -s '$image' '${image.name}'.ome.tiff; 11 ln -s $image input.ome.tiff;
12 ln -s '$primary_mask' '${primary_mask.name}'.ome.tiff; 12 ln -s $primary_mask primary_mask.tiff;
13 #for $mask in $supp_masks: 13 #if $supp_masks
14 ln -s '$mask' '${mask.name}'.ome.tiff; 14 ln -s $supp_masks supp_mask.tiff;
15 #end for 15 #end if
16 16
17 mkdir ./tool_out; 17 mkdir ./tool_out;
18 18
19 @CMD_BEGIN@ 19 @CMD_BEGIN@
20 20
21 python \$QUANT_PATH 21 python \$QUANT_PATH
22 --masks 22 --masks
23 '${primary_mask.name}'.ome.tiff 23 primary_mask.tiff
24 #if $supp_masks 24 #if $supp_masks
25 #for $mask in $supp_masks: 25 supp_mask.tiff
26 '${mask.name}'.ome.tiff
27 #end for
28 #end if 26 #end if
29 27
30 --image '${image.name}'.ome.tiff 28 --image input.ome.tiff
31 --output ./tool_out 29 --output ./tool_out
32 30
33 #if $mask_props 31 #if $mask_props
34 --mask_props $mask_props 32 --mask_props $mask_props
35 #end if 33 #end if
36 #if $intensity_props 34 #if $intensity_props
37 --intensity_props $intensity_props 35 --intensity_props $intensity_props
38 #end if 36 #end if
39 37
40 --channel_names '$channel_names'; 38 --channel_names '$channel_names';
41 39
42 cp tool_out/*cellMasks.csv cellMasks.csv 40 cp tool_out/*primary_mask.csv primary_mask.csv
43 ]]></command> 41 ]]></command>
44 42
45 <inputs> 43 <inputs>
46 <param name="image" type="data" format="tiff" label="Registered TIFF"/> 44 <param name="image" type="data" format="tiff" label="Registered TIFF"/>
47 <param name="primary_mask" type="data" format="tiff" label="Primary Cell Mask"/> 45 <param name="primary_mask" type="data" format="tiff" label="Primary Cell Mask"/>
48 <param name="supp_masks" type="data" multiple="true" optional="true" format="tiff" label="Additional Cell Masks"/> 46 <param name="supp_masks" type="data" optional="true" format="tiff" label="Additional Cell Masks"/>
49 <param name="channel_names" type="data" format="csv" label="Marker Channels"/> 47 <param name="channel_names" type="data" format="csv" label="Marker Channels"/>
50 <param name="mask_props" type="text" label="Mask Metrics" help="Space separated list of additional metrics to be calculated for every mask."/> 48 <param name="mask_props" type="text" label="Mask Metrics" help="Space separated list of additional metrics to be calculated for every mask."/>
51 <param name="intensity_props" type="text" label="Intensity Metrics" help="Space separated list of additional metrics to be calculated for every marker separately."/> 49 <param name="intensity_props" type="text" label="Intensity Metrics" help="Space separated list of additional metrics to be calculated for every marker separately."/>
52 </inputs> 50 </inputs>
53 51
54 <outputs> 52 <outputs>
55 <data format="csv" name="cellmask" from_work_dir="cellMasks.csv" label="CellMaskQuant"/> 53 <data format="csv" name="cellmask" from_work_dir="primary_mask.csv" label="CellMaskQuant"/>
56 <collection type="list" name="quantification" label="${tool.name} on ${on_string}"> 54 <collection type="list" name="quantification" label="${tool.name} on ${on_string}">
57 <discover_datasets pattern="__designation_and_ext__" format="csv" directory="tool_out/" visible="true"/> 55 <discover_datasets pattern="__designation_and_ext__" format="csv" directory="tool_out/" visible="true"/>
58 </collection> 56 </collection>
59 </outputs> 57 </outputs>
60 <help><![CDATA[ 58 <help><![CDATA[
61 # Single cell quantification 59 # Single cell quantification
62 Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output. 60 Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output.