Mercurial > repos > perssond > quantification

comparison quantification.xml @ 0:928db0f952e3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
author perssond
date Fri, 12 Mar 2021 00:19:24 +0000
parents
children aba3655fdef0
comparison
equal deleted inserted replaced
-1:000000000000 0:928db0f952e3
1 <tool id="quantification" name="Quantification" version="@VERSION@.5" profile="17.09">
2 <description>Single cell quantification, a module for single-cell data extraction given a segmentation mask and multi-channel image.</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 ln -s '$image' '${image.name}'.ome.tiff;
12 ln -s '$primary_mask' '${primary_mask.name}'.ome.tiff;
13 #for $mask in $supp_masks:
14 ln -s '$mask' '${mask.name}'.ome.tiff;
15 #end for
16
17 mkdir ./tool_out;
18
19 @CMD_BEGIN@
20
21 --masks
22 '${primary_mask.name}'.ome.tiff
23 #if $supp_masks
24 #for $mask in $supp_masks:
25 '${mask.name}'.ome.tiff
26 #end for
27 #end if
28
29 --image '${image.name}'.ome.tiff
30 --output ./tool_out
31 --channel_names '$channel_names';
32
33 mv ./tool_out/*.csv ./tool_out/quantified.csv;
34 ]]></command>
35
36 <inputs>
37 <param name="image" type="data" format="tiff" label="Registered TIFF"/>
38 <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"/>
40 <param name="channel_names" type="data" format="csv" label="Marker Channels"/>
41 </inputs>
42
43 <outputs>
44 <data format="csv" name="quant_out" from_work_dir="./tool_out/quantified.csv" label="${tool.name} on ${on_string}"/>
45 </outputs>
46 <help><![CDATA[
47 # 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.
49
50 **CommandSingleCellExtraction.py**:
51
52 * `--masks` Paths to where masks are stored (Ex: ./segmentation/cellMask.tif) -> If multiple masks are selected the first mask will be used for spatial feature extraction but all will be quantified
53
54 * `--image` Path to image(s) for quantification. (Ex: ./registration/*.h5) -> works with .h(df)5 or .tif(f)
55
56 * `--output` Path to output directory. (Ex: ./feature_extraction)
57
58 * `--channel_names` csv file containing the channel names for the z-stack (Ex: ./my_channels.csv)
59
60 # Run script
61 `python CommandSingleCellExtraction.py --masks ./segmentation/cellMask.tif ./segmentation/membraneMask.tif --image ./registration/Exemplar_001.h5 --output ./feature_extraction --channel_names ./my_channels.csv`
62
63 # Main developer
64 Denis Schapiro (https://github.com/DenisSch)
65
66 Joshua Hess (https://github.com/JoshuaHess12)
67
68 Jeremy Muhlich (https://github.com/jmuhlich)
69 ]]></help>
70 <expand macro="citations" />
71 </tool>