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annotate mcmicro_to_anndata.xml @ 1:8ca435ec19be draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit d20d6f5d08b43de71182459f8a6452c564a5becc
author goeckslab
date Mon, 29 Aug 2022 23:54:52 +0000
parents 2a3152751ca8
children 4c767e1a9e7c
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2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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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@">
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2 <description>to be used in scimap/scanpy</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="scimap_requirements" />
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7 <expand macro="macro_stdio" />
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command>
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10 <![CDATA[
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11 python '$__tool_directory__/mcmicro_to_anndata.py'
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12 --inputs '$inputs'
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13 --outfile '$outfile'
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14
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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15 ]]>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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16 </command>
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17 <configfiles>
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18 <inputs name="inputs" data_style="paths"/>
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19 </configfiles>
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20 <inputs>
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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21 <param argument="image_path" type="data" format="tabular,csv" multiple="false" label="Select the input image or images" />
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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
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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
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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
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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
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26 If multiple images are passed, just use the string that appears in the first image." />
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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
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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
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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
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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
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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
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32 <param argument="custom_imageid" optional="true" type="text" label="Custom image ID" help="By default the name of the CSV file is used." />
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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." />
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34 </section>
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35 </inputs>
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36 <outputs>
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37 <data format="h5ad" name="outfile" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="image_path" value="mcmicro_output.csv" ftype="csv" />
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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
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43 <output name="outfile" file="tutorial_data.h5ad" compare="sim_size" delta="5" />
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44 </test>
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45 </tests>
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46 <help>
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47 <![CDATA[
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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48 **What it does**
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49
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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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.
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51
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52
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53 **Return**
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54
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55 Anndata.
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56
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57 ]]>
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58 </help>
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59 <citations>
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60 </citations>
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61 </tool>