Mercurial > repos > goeckslab > scimap_phenotyping

annotate scimap_phenotyping.xml @ 3:3a441d347a46 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/tree/main/tools/scimap commit 49210b00535415865694ddbec16238d8cf5e6bb0
author goeckslab
date Wed, 26 Jun 2024 15:27:07 +0000
parents ce22e846c5e4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
1 <tool id="scimap_phenotyping" name="Single Cell Phenotyping" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
2 <description>using scimap</description>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
3 <macros>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
4 <import>main_macros.xml</import>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
5 </macros>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
6
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
7 <expand macro="scimap_requirements"/>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
8 <expand macro="macro_stdio" />
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
9 <version_command>echo "@VERSION@"</version_command>
2
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
10 <command detect_errors="aggressive">
0
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
11 <![CDATA[
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
12 python '$__tool_directory__/scimap_phenotyping.py'
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
13 --adata '$anndata'
2
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
14 #if $log
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
15 --log
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
16 #end if
0
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
17 #if $manual_gates
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
18 --manual_gates '$manual_gates'
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
19 --manual_gates_ext '${manual_gates.ext}'
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
20 #end if
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
21 --gating_workflow '$gating_workflow'
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
22 --gating_workflow_ext '${gating_workflow.ext}'
2
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
23 --random_state '$random_state'
0
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
24 --output '$output'
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
25
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
26 ]]>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
27 </command>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
28 <configfiles>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
29 <inputs name="inputs" />
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
30 </configfiles>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
31 <inputs>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
32 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
2
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
33 <param name="log" type="boolean" checked="true" label="Whether to log the data prior to rescaling" />
0
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
34 <param name="manual_gates" type="data" format="tabular,csv" optional="true" label="Select the dataset containing manual gate information" help="First column as markers and second column as the gate values in log1p scale. If a marker is not included, auto gating
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
35 based on gaussian mixture modeling will be executed. Optional."/>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
36 <param name="gating_workflow" type="data" format="tabular,csv" label="Select the dataset containing gating workflow" />
2
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
37 <param name="random_state" type="integer" value="0" optional="true" label="Set seed used by the random number generator for GMM" />
0
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
38 </inputs>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
39 <outputs>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
40 <data format="h5ad" name="output" />
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
41 </outputs>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
42 <tests>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
43 <test>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
44 <param name="anndata" value="tutorial_data.h5ad" ftype="h5ad" />
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
45 <param name="manual_gates" value="manual_gates.csv" ftype="csv" />
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
46 <param name="gating_workflow" value="phenotype_workflow.csv" ftype="csv" />
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
47 <output name="output">
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
48 <assert_contents>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
49 <has_h5_keys keys="obs/phenotype" />
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
50 </assert_contents>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
51 </output>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
52 </test>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
53 </tests>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
54 <help>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
55 <![CDATA[
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
56 **What it does**
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
57
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
58 This tool generates single cell phenotyping using either manual gating or auto gating (gaussian mixture modeling) implemented in Scimap.
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
59
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
60 **Input**
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
61
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
62 AnnData.
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
63
2
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
64 **Important Note**
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
65
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
66 If adata.raw.X exists, it will be used. If adata.raw.X does not exist, adata.X is used
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
67
0
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
68 **Output**
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
69
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
70 Anndata with "obs/phenotype" added.
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
71
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
72
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
73 ]]>
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
74 </help>
2
ce22e846c5e4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
75 <expand macro="citations" />
0
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
76 </tool>