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comparison mcmicro_to_anndata.xml @ 0:2a3152751ca8 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
author goeckslab
date Tue, 19 Jul 2022 20:29:59 +0000
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1 <tool id="scimap_mcmicro_to_anndata" name="Convert McMicro Output to Anndata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>to be used in scimap/scanpy</description>
3 <macros>
4 <import>main_macros.xml</import>
5 </macros>
6 <expand macro="scimap_requirements" />
7 <expand macro="macro_stdio" />
8 <version_command>echo "@VERSION@"</version_command>
9 <command>
10 <![CDATA[
11 python '$__tool_directory__/mcmicro_to_anndata.py'
12 --inputs '$inputs'
13 --outfile '$outfile'
14
15 ]]>
16 </command>
17 <configfiles>
18 <inputs name="inputs" data_style="paths"/>
19 </configfiles>
20 <inputs>
21 <param argument="image_path" type="data" format="tabular,csv" multiple="false" label="Select the input image or images" />
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." />
23 <section name="options" title="Advanced Options" expanded="False">
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." />
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.
26 If multiple images are passed, just use the string that appears in the first image." />
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" />
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." />
29 <param argument="CellId" optional="true" type="text" value="CellID" label="Name of the column that contains the cell ID" />
30 <param argument="unique_CellId" optional="true" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Whether to use unique name for cells/rows" />
31 <param argument="split" optional="true" type="text" value="X_centroid" label="Column name to split the csv into counts table and meta data" />
32 <param argument="custom_imageid" optional="true" type="text" label="Custom image ID" help="By default the name of the CSV file is used." />
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." />
34 </section>
35 </inputs>
36 <outputs>
37 <data format="h5ad" name="outfile" />
38 </outputs>
39 <tests>
40 <test>
41 <param name="image_path" value="mcmicro_output.csv" ftype="csv" />
42 <param name="drop_markers" value="PERK,NOS2,BG1,BG2,BG3,ACTIN" />
43 <output name="outfile" file="tutorial_data.h5ad" compare="sim_size" delta="5" />
44 </test>
45 </tests>
46 <help>
47 <![CDATA[
48 **What it does**
49
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.
51
52
53 **Return**
54
55 Anndata.
56
57 ]]>
58 </help>
59 <citations>
60 </citations>
61 </tool>