annotate scimap_spatial.xml @ 3:472780baf150 draft

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author goeckslab
date Wed, 26 Jun 2024 15:26:49 +0000
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1 <tool id="scimap_spatial" name="Spatial Analysis Tools" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from Scimap</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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7 <expand macro="scimap_requirements"/>
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8 <expand macro="macro_stdio" />
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9 <version_command>echo "@VERSION@"</version_command>
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10 <command detect_errors="aggressive">
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11 <![CDATA[
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12 python '$__tool_directory__/scimap_spatial.py'
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13 --inputs '$inputs'
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14 --anndata '$anndata'
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15 --output '$output'
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16
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17 ]]>
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18 </command>
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19 <configfiles>
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20 <inputs name="inputs" />
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21 </configfiles>
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22 <inputs>
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23 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
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24 <conditional name="analyses">
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25 <param name="selected_tool" type="select" label="Select an analysis">
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26 <option value="cluster">Cluster</option>
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27 <option value="spatial_aggregate">Spatial Aggregate -- find regions of aggregration of similar cells</option>
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28 <option value="spatial_count" selected="true">Spatial Count -- compute a neighbourhood matrix using any categorical variables (e.g. cell-types)</option>
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29 <option value="spatial_distance">Spatial Distance -- calculate the average shortest between phenotypes or clusters of interest</option>
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30 <option value="spatial_expression">Spatial Expression -- o compute a neighbourhood weighted matrix based on the expression values</option>
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31 <option value="spatial_interaction">Spatial Interaction -- computes how likely celltypes are found next to each another compared to random background</option>
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32 <option value="spatial_lda">Spatial LDA -- compute a neighbourhood matrix using any categorical variable and then perform Latent Dirichlet Allocation (LDA) modelling</option>
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33 <option value="spatial_pscore">Spatial pscore -- a scoring system to evaluate user defined proximity between cell types</option>
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34 </param>
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35 <when value="cluster">
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36 <param name="method" type="select" label="Select the clustering method">
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37 <option value="kmeans" selected="true">kmeans</option>
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38 <option value="phenograph">phenograph</option>
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39 <option value="leiden">leiden</option>
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40 </param>
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41 <section name="options" title="Advanced Options" expanded="false">
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42 <param argument="subset_genes" type="text" value="" optional="true" label="Type in a list of genes that should be included for the purpose of clustering" help="Optional. Comma delimited. By default the algorithm uses all genes in the dataset." />
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43 <param argument="sub_cluster" type="boolean" checked="false" optional="true" label="Whether to do sub-clustering on existing clustering or phenotyping " />
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44 <param argument="sub_cluster_column" type="text" value="phenotype" optional="true" label="Type in the name of a column to be sub-clustered" help="This is only required when sub_cluster is set to True." />
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45 <param argument="sub_cluster_group" type="text" value="" optional="true" label="Type in a list of group names within the sub-cluster column" help="Optional. Comma delimited. By default the program will sub-cluster all groups within column passed through the argument sub_cluster_column." />
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46 <param argument="k" type="integer" value="10" optional="true" label="Number of clusters to return when using K-Means clustering" />
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47 <param argument="n_pcs" type="integer" value="" optional="true" label="Number of PC's to be used in leiden clustering" help="By default it uses all PC's" />
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48 <param argument="resolution" type="float" value="1" optional="true" label="A parameter value controlling the coarseness of the clustering" help="Higher values lead to more clusters." />
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49 <param argument="phenograph_clustering_metric" type="select" label="Distance metric to define nearest neighbors">
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50 <option value="euclidean" selected="true">euclidean</option>
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51 <option value="cityblock">cityblock</option>
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52 <option value="cosine">cosine</option>
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53 <option value="manhattan">manhattan</option>
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54 <option value="braycurtis">braycurtis</option>
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55 <option value="canberra">canberra</option>
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56 <option value="chebyshev">chebyshev</option>
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57 <option value="correlation">correlation</option>
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58 <option value="dice">dice</option>
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59 <option value="hamming">hamming</option>
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60 <option value="jaccard">jaccard</option>
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61 <option value="mahalanobis">mahalanobis</option>
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62 <option value="minkowski">minkowski</option>
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63 <option value="rogerstanimoto">rogerstanimoto</option>
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64 <option value="russellrao">russellrao</option>
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65 <option value="seuclidean">seuclidean</option>
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66 <option value="sokalmichener">sokalmichener</option>
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67 <option value="sokalsneath">sokalsneath</option>
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68 <option value="sqeuclidean">sqeuclidean</option>
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69 <option value="yule">yule</option>
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70 </param>
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71 <param argument="nearest_neighbors" type="integer" value="30" optional="true" label="Number of nearest neighbors to use in first step of graph construction" help="This parameter is used both in leiden and phenograph clustering." />
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72 <param argument="use_raw" type="boolean" checked="true" optional="true" label="Whether to use raw data for clustering" help=" If False, normalized/scaled data within adata.X will be used." />
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73 <!-- <param argument="log" type="boolean" checked="true" optional="true" label="Whether to log the raw data" help="Set use_raw = True for this to take effect." /> -->
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74 <param argument="random_state" type="integer" value="0" optional="true" help="Used to change the initialization of the optimization." />
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75 <param argument="collapse_labels" type="boolean" checked="false" optional="true" help="While sub clustering only a few phenotypes/clusters, this argument helps to group all the other phenotypes/clusters into a single category- Helps in visualisation." />
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76 <param argument="label" type="text" value="" optional="true" label="Column name for the returned data" help="Stored in adata.obs. The default is adata.obs [method used]." />
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77 <!-- <param argument="output_dir"> -->
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78 </section>
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79 </when>
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80 <when value="spatial_aggregate">
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81 <expand macro="scimap_spatial_options" label="spatial_aggregate">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
82 <param argument="phenotype" type="text" value="phenotype" optional="flase" label="Column name of the column containing the phenotype information" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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83 <param argument="purity" type="integer" value="60" min="1" max="100" label="Percent purity of neighbouring cells" help="e.g. if 60 is chosen, every neighbourhood is tested such that if a particular phenotype makes up greater than 60% of the total population it is annotated to be an aggregate of that particular phenotype." />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
84 <param argument="method" type="select" label="Select the method">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
85 <option value="radius" selected="true">radius</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
86 <option value="knn">knn</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
87 </param>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
88 <param argument="radius" type="integer" value="30" optional="true" label="The radius used to define a local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
89 <param argument="knn" type="integer" value="10" optional="true" label="Number of cells considered for defining the local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
90 </expand>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
91 </when>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
92 <when value="spatial_count">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
93 <expand macro="scimap_spatial_options" label="spatial_count">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
94 <param argument="phenotype" type="text" value="phenotype" optional="flase" label="Column name of the column containing the phenotype information" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
95 <param argument="method" type="select" label="Select the method">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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96 <option value="radius" selected="true">radius</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
97 <option value="knn">knn</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
98 </param>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
99 <param argument="radius" type="integer" value="30" optional="true" label="The radius used to define a local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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100 <param argument="knn" type="integer" value="10" optional="true" label="Number of cells considered for defining the local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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101 </expand>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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102 </when>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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103 <when value="spatial_distance">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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104 <expand macro="scimap_spatial_options">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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105 <param argument="phenotype" type="text" value="phenotype" optional="flase" label="Column name of the column containing the phenotype information" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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106 </expand>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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107 </when>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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108 <when value="spatial_expression">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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109 <expand macro="scimap_spatial_options" label="spatial_expression">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
110 <param argument="method" type="select" label="Select the method">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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111 <option value="radius" selected="true">radius</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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112 <option value="knn">knn</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
113 </param>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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114 <param argument="radius" type="integer" value="30" optional="true" label="The radius used to define a local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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115 <param argument="knn" type="integer" value="10" optional="true" label="Number of cells considered for defining the local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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116 <param argument="use_raw" type="boolean" checked="true" optional="true" label="Whether to use raw data for clustering" help=" If False, normalized/scaled data within adata.X will be used." />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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117 <!-- <param argument="log" type="boolean" checked="true" optional="true" label="Whether to log the raw data" help="Set use_raw = True for this to take effect." /> -->
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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118 </expand>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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119 </when>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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120 <when value="spatial_interaction">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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121 <expand macro="scimap_spatial_options" label="spatial_interaction">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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122 <param argument="phenotype" type="text" value="phenotype" optional="flase" label="Column name of the column containing the phenotype information" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
123 <param argument="method" type="select" label="Select the method">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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124 <option value="radius" selected="true">radius</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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125 <option value="knn">knn</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
126 </param>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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127 <param argument="radius" type="integer" value="30" optional="true" label="The radius used to define a local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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128 <param argument="knn" type="integer" value="10" optional="true" label="Number of cells considered for defining the local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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129 <param argument="permutation" type="integer" value="1000" optional="true" label="The number of permutations to be performed for calculating the P-Value" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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130 <param argument="pval_method" type="select" label="Select a method to calculate the P-values">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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131 <option value="zscore" selected="true">zscore</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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132 <option value="histocat">histocat</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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133 </param>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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134 </expand>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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135 </when>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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136 <when value="spatial_lda">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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137 <expand macro="scimap_spatial_options" label="spatial_lda">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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138 <param argument="phenotype" type="text" value="phenotype" optional="flase" label="Column name of the column containing the phenotype information" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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139 <param argument="method" type="select" label="Select the method">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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140 <option value="radius" selected="true">radius</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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141 <option value="knn">knn</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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142 </param>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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143 <param argument="radius" type="integer" value="30" optional="true" label="The radius used to define a local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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144 <param argument="knn" type="integer" value="10" optional="true" label="Number of cells considered for defining the local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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145 <param argument="num_motifs" type="integer" value="10" optional="true" label="The number of requested latent motifs to be extracted from the training corpus" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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146 <param argument="random_state" type="integer" value="0" optional="true" label="The seed number for random state" />
3
472780baf150 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 49210b00535415865694ddbec16238d8cf5e6bb0
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147 <param argument="max_weight_assignment" type="boolean" checked="false" optional="true" label="Assign cells to motifs based on maximum LDA weight" />
0
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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148 </expand>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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149 </when>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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150 <when value="spatial_pscore">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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151 <expand macro="scimap_spatial_options" label="spatial_pscore">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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152 <param argument="proximity" type="text" value="" optional="false" label="Type in the list of cell-types for which the proximity score needs to calculated" help="Comma delimited. e.g.: CellType-A,CellType-B." />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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153 <param argument="score_by" type="text" value="imageid" optional="true" label="Column name containing region's of interest for score comparison" help="Optional. By default the score is calculated across the entire image." />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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154 <param argument="phenotype" type="text" value="phenotype" optional="flase" label="Column name of the column containing the phenotype information" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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155 <param argument="method" type="select" label="Select the method">
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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156 <option value="radius" selected="true">radius</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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157 <option value="knn">knn</option>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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158 </param>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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159 <param argument="radius" type="integer" value="20" optional="true" label="The radius used to define a local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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160 <param argument="knn" type="integer" value="3" optional="true" label="Number of cells considered for defining the local neighbhourhood" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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161 </expand>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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162 </when>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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163 </conditional>
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164 </inputs>
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165 <outputs>
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166 <data format="h5ad" name="output" label="Scimap.tools.${analyses.selected_tool} on ${on_string}" />
3
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167 <collection name="tabular_outputs" type="list" label="Tabular outputs from Scimap.tools.${analyses.selected_tool} on ${on_string}">
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168 <data format="tabular" name="lda_weights" from_work_dir="lda_weights.txt" label="LDA weights from Scimap.tools.${analyses.selected_tool} on ${on_string}" />
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169 <data format="tabular" name="lda_probabilities" from_work_dir="lda_probabilities.txt" label="LDA probabilites from Scimap.tools.${analyses.selected_tool} on ${on_string}" />
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170 <filter>analyses['selected_tool'] == 'spatial_lda'</filter>
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171 </collection>
0
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172 </outputs>
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173 <tests>
3
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174 <test expect_num_outputs="1">
2
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175 <param name="anndata" value="tutorial_data_pheno.h5ad" />
0
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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176 <conditional name="analyses">
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177 <param name="selected_tool" value="cluster" />
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178 <param name="method" value="kmeans" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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179 </conditional>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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180 <output name="output">
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181 <assert_contents>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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182 <has_h5_keys keys="obs/kmeans" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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183 </assert_contents>
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184 </output>
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185 </test>
3
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186 <test expect_num_outputs="1">
0
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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187 <param name="anndata" value="tutorial_data_pheno.h5ad" />
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188 <conditional name="analyses">
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189 <param name="selected_tool" value="spatial_aggregate" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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190 </conditional>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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191 <output name="output">
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192 <assert_contents>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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193 <has_h5_keys keys="obs/spatial_aggregate" />
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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194 </assert_contents>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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195 </output>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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196 </test>
3
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197 <test expect_num_outputs="4">
472780baf150 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 49210b00535415865694ddbec16238d8cf5e6bb0
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198 <param name="anndata" value="tutorial_data_pheno.h5ad" />
472780baf150 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 49210b00535415865694ddbec16238d8cf5e6bb0
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199 <conditional name="analyses">
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200 <param name="selected_tool" value="spatial_lda" />
472780baf150 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 49210b00535415865694ddbec16238d8cf5e6bb0
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201 <section name="options">
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202 <param name="max_weight_assignment" value="True" />
472780baf150 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 49210b00535415865694ddbec16238d8cf5e6bb0
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203 </section>
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204 </conditional>
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205 <output name="output">
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206 <assert_contents>
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207 <has_h5_keys keys="obs/neighborhood_motif" />
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208 </assert_contents>
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209 </output>
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210 <output_collection name="tabular_outputs" type="list">
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211 <element name="lda_weights">
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212 <assert_contents>
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213 <has_n_lines n="500" />
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214 <has_n_columns n="12" />
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215 </assert_contents>
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216 </element>
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217 <element name="lda_probabilities">
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218 <assert_contents>
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219 <has_n_lines n="11" />
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220 <has_n_columns n="15" />
472780baf150 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 49210b00535415865694ddbec16238d8cf5e6bb0
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221 </assert_contents>
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222 </element>
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223 </output_collection>
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224 </test>
0
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225 </tests>
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226 <help>
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227 <![CDATA[
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228 **What it does**
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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229
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230 This tool does various single cell spatial analyses with Scimap.
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231
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232 **Input**
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233
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234 AnnData.
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235
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236 **Output**
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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237
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238 Anndata with a corresponding key added.
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239
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240
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241 ]]>
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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242 </help>
2
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243 <expand macro="citations" />
0
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244 </tool>