annotate mcmicro_to_anndata.xml @ 2:4c767e1a9e7c draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
author goeckslab
date Mon, 10 Jun 2024 18:45:21 +0000
parents 2a3152751ca8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
1 <tool id="scimap_mcmicro_to_anndata" name="Convert McMicro Output to Anndata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
2 <description>to be used in scimap/scanpy</description>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
3 <macros>
2a3152751ca8 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>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
5 </macros>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
6 <expand macro="scimap_requirements" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
7 <expand macro="macro_stdio" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
8 <version_command>echo "@VERSION@"</version_command>
2
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
9 <command detect_errors="aggressive">
0
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
10 <![CDATA[
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
11 python '$__tool_directory__/mcmicro_to_anndata.py'
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
12 --inputs '$inputs'
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
13 --outfile '$outfile'
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
14
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
15 ]]>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
16 </command>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
17 <configfiles>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
18 <inputs name="inputs" data_style="paths"/>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
19 </configfiles>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
20 <inputs>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
21 <param argument="image_path" type="data" format="tabular,csv" multiple="false" label="Select the input image or images" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
22 <param argument="drop_markers" type="text" optional="true" label="List of markers to drop from the analysis" help="No quotes, separated by comma. e.g. CD3D, CD20." />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
23 <section name="options" title="Advanced Options" expanded="False">
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
24 <param argument="remove_dna" optional="true" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Whether to Remove the DNA channels from the final output" help="Looks for channels with the string 'dna' in it." />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
25 <param argument="remove_string_from_name" type="text" optional="true" label="Remove string from name" help="Used to clean up channel names. If a string is given, that particular string will be removed from all marker names.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
26 If multiple images are passed, just use the string that appears in the first image." />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
27 <param argument="log" optional="true" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Whether to log the data" help="log1p transformation will be applied" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
28 <param argument="random_sample" optional="true" type="integer" label="The number of random sampling" help="Randomly sub-sample the data with the desired number of cells." />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
29 <param argument="CellId" optional="true" type="text" value="CellID" label="Name of the column that contains the cell ID" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
30 <param argument="unique_CellId" optional="true" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Whether to use unique name for cells/rows" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
31 <param argument="split" optional="true" type="text" value="X_centroid" label="Column name to split the csv into counts table and meta data" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
32 <param argument="custom_imageid" optional="true" type="text" label="Custom image ID" help="By default the name of the CSV file is used." />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
33 <param argument="min_cells" optional="true" type="integer" label="Minimum number of cells" help="If these many cells are not in the image, the image will be dropped. Particulary useful when importing multiple images." />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
34 </section>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
35 </inputs>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
36 <outputs>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
37 <data format="h5ad" name="outfile" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
38 </outputs>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
39 <tests>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
40 <test>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
41 <param name="image_path" value="mcmicro_output.csv" ftype="csv" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
42 <param name="drop_markers" value="PERK,NOS2,BG1,BG2,BG3,ACTIN" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
43 <output name="outfile" file="tutorial_data.h5ad" compare="sim_size" delta="5" />
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
44 </test>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
45 </tests>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
46 <help>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
47 <![CDATA[
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
48 **What it does**
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
49
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
50 The tool converts the quantification output from [mcmicro](https://mcmicro.org/) to Anndata which is needed for downstrem analyses, such as phenotyping, neighbourhood identification, and so on.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
51
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
52
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
53 **Return**
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
54
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
55 Anndata.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
56
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
57 ]]>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
58 </help>
2
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents: 0
diff changeset
59 <expand macro="citations" />
0
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
60 </tool>