Mercurial > repos > perssond > quantification

annotate quantification.xml @ 5:3a916c4e9f5f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/tools-mti commit 0762a583dd9d7333f9b039bc06003caaff0f2103
author goeckslab
date Wed, 28 Dec 2022 21:19:44 +0000
parents 261464223fa3
children e11d5fafd0cc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
1 <tool id="quantification" name="MCQUANT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
2 <description>a module for single-cell data extraction</description>
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
3 <macros>
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
4 <import>macros.xml</import>
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
5 </macros>
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
6 <expand macro="requirements"/>
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
7 <expand macro="version_cmd"/>
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
8
5
3a916c4e9f5f planemo upload for repository https://github.com/goeckslab/tools-mti commit 0762a583dd9d7333f9b039bc06003caaff0f2103
goeckslab
parents: 4
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
10 ln -s '$image' 'input.ome.tiff' &&
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
11 ln -s '$primary_mask' 'primary_mask.tiff' &&
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
12 #if $supp_mask
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
13 ln -s '$supp_mask' 'supp_mask.tiff' &&
2
46b897eb2c8e "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"
watsocam
parents: 1
diff changeset
14 #end if
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
15
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
16 mkdir './tool_out' &&
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
17
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
18 @CMD_BEGIN@
2
46b897eb2c8e "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"
watsocam
parents: 1
diff changeset
19
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
20 --masks 'primary_mask.tiff'
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
21 #if $supp_mask
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
22 'supp_mask.tiff'
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
23 #end if
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
24
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
25 --image 'input.ome.tiff'
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
26 --output './tool_out'
2
46b897eb2c8e "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"
watsocam
parents: 1
diff changeset
27
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
28 #if str($mask_props).strip()
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
29 --mask_props '$mask_props'
1
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
watsocam
parents: 0
diff changeset
30 #end if
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
31 #if str($intensity_props).strip()
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
32 --intensity_props '$intensity_props'
1
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
watsocam
parents: 0
diff changeset
33 #end if
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
watsocam
parents: 0
diff changeset
34
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
35 --channel_names '$channel_names' &&
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
36
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
37 #if $supp_mask
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
38 mv tool_out/*supp_mask.csv supp_mask.csv &&
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
39 #end if
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
40
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
41 mv tool_out/*primary_mask.csv primary_mask.csv
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
42 ]]></command>
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
43
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
44 <inputs>
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
45 <param name="image" type="data" format="tiff" label="Registered TIFF"/>
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
46 <param name="primary_mask" type="data" format="tiff" label="Primary Mask"/>
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
47 <param name="supp_mask" type="data" optional="true" format="tiff" label="Additional Mask"/>
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
48 <param name="channel_names" type="data" format="csv" label="Marker Channels"/>
1
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
watsocam
parents: 0
diff changeset
49 <param name="mask_props" type="text" label="Mask Metrics" help="Space separated list of additional metrics to be calculated for every mask."/>
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
watsocam
parents: 0
diff changeset
50 <param name="intensity_props" type="text" label="Intensity Metrics" help="Space separated list of additional metrics to be calculated for every marker separately."/>
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
51 </inputs>
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
52
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
53 <outputs>
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
54 <data format="csv" name="cellmask" from_work_dir="primary_mask.csv" label="Primary Mask Quantification"/>
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
55 <data format="csv" name="suppmask" from_work_dir="supp_mask.csv" label="Supplemental Mask Quantification">
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
56 <filter>supp_mask</filter>
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
57 </data>
1
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
watsocam
parents: 0
diff changeset
58 </outputs>
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
59 <tests>
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
60 <test>
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
61 <param name="image" value="test.tiff" />
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
62 <param name="primary_mask" value="mask.tiff" />
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
63 <param name="supp_mask" value="supp_mask.tiff" />
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
64 <param name="channel_names" value="channels.csv" />
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
65 <output name="cellmask" ftype="csv">
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
66 <assert_contents>
5
3a916c4e9f5f planemo upload for repository https://github.com/goeckslab/tools-mti commit 0762a583dd9d7333f9b039bc06003caaff0f2103
goeckslab
parents: 4
diff changeset
67 <has_n_lines n="264" delta="1" />
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
68 </assert_contents>
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
69 </output>
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
70 <output name="suppmask" ftype="csv">
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
71 <assert_contents>
5
3a916c4e9f5f planemo upload for repository https://github.com/goeckslab/tools-mti commit 0762a583dd9d7333f9b039bc06003caaff0f2103
goeckslab
parents: 4
diff changeset
72 <has_n_lines n="264" delta="1" />
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
73 </assert_contents>
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
74 </output>
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
75 </test>
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
76 </tests>
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
77 <help><![CDATA[
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
78
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
79 --------
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
80 MCQUANT
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
81 --------
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
82 **MCQUANT** module for single cell quantification given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output.
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
83
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
84 **Inputs**
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
85 1. A fully stitched and registered image in .ome.tif format. Nextflow will use images in the registration/ and dearray/ subfolders as appropriate.
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
86 2. One or more segmentation masks in .tif format. Nextflow will use files in the segmentation/ subfolder within the project.
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
87 3. A .csv file containing a marker_name column specifying names of individual channels. Nextflow will look for this file in the project directory.
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
88
4
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
89 **Outputs**
261464223fa3 planemo upload for repository https://github.com/goeckslab/tools-mti commit ed91d9e0dd189986b5c31fe23f5f78bd8765d862
goeckslab
parents: 3
diff changeset
90 A cell-by-feature table mapping Cell IDs to marker expression and morphological features (including x,y coordinates).
0
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
91
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
92 ]]></help>
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
93 <expand macro="citations" />
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
perssond
parents:
diff changeset
94 </tool>