Mercurial > repos > iuc > snapatac2_clustering

annotate dimension_reduction_clustering.xml @ 0:af821711b356 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
author iuc
date Thu, 16 May 2024 13:15:57 +0000
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children 8f8bef61fd0b
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af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1 <tool id="snapatac2_clustering" name="SnapATAC2 Clustering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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2 <description>and dimension reduction</description>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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3 <macros>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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4 <import>macros.xml</import>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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5 </macros>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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6 <requirements>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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7 <expand macro="requirements"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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8 </requirements>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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9 <command detect_errors="exit_code"><![CDATA[
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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10 export NUMBA_CACHE_DIR="\${TEMP:-/tmp}";
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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11 @PREP_ADATA@
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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12 @CMD@
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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13 ]]></command>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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14 <configfiles>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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15 <configfile name="script_file"><![CDATA[
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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16
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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17 @CMD_imports@
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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18 @CMD_read_inputs@
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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19
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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20 #if $method.method == 'tl.spectral'
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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21 #if $method.features
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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22 with open('$method.features') as f:
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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23 features_mask = [x.lower().capitalize() == "True" for x in f.read().splitlines()]
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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24 #end if
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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25 sa.tl.spectral(
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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26 adata,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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27 n_comps = $method.n_comps,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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28 #if $method.features
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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29 features = features_mask,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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30 #end if
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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31 random_state = $method.random_state,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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32 #if $method.sample_size
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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33 sample_size = $method.sample_size,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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34 #end if
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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35 chunk_size = $method.chunk_size,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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36 distance_metric = '$method.distance_metric',
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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37 weighted_by_sd = $method.weighted_by_sd,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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38 inplace = True
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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39 )
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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40
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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41 #else if $method.method == 'tl.umap'
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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42 sa.tl.umap(
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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43 adata,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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44 n_comps = $method.n_comps,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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45 #if $method.use_dims != ''
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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46 #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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47 use_dims=$dims,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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48 #end if
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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49 use_rep = '$method.use_rep',
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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50 key_added = '$method.key_added',
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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51 random_state = $method.random_state,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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52 inplace = True
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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53 )
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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54
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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55 #else if $method.method == 'pp.knn'
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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56 sa.pp.knn(
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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57 adata,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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58 n_neighbors = $method.n_neighbors,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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59 #if $method.use_dims != ''
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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60 #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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61 use_dims=$dims,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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62 #end if
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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63 use_rep = '$method.use_rep',
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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64 method = '$method.algorithm',
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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65 inplace = True,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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66 random_state = $method.random_state
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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67 )
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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68
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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69 #else if $method.method == 'tl.dbscan'
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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70 sa.tl.dbscan(
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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71 adata,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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72 eps = $method.eps,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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73 min_samples = $method.min_samples,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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74 leaf_size = $method.leaf_size,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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75 use_rep = '$method.use_rep',
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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76 key_added = '$method.key_added'
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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77 )
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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78
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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79 #else if $method.method == 'tl.hdbscan'
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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80 sa.tl.hdbscan(
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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81 adata,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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82 min_cluster_size = $method.min_cluster_size,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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83 #if $method.min_samples
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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84 min_samples = $method.min_samples,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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85 #end if
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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86 cluster_selection_epsilon = $method.cluster_selection_epsilon,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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87 alpha = $method.alpha,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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88 cluster_selection_method = '$method.cluster_selection_method',
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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89 random_state = $method.random_state,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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90 use_rep = '$method.use_rep',
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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91 key_added = '$method.key_added'
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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92 )
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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93
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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94 #else if $method.method == 'tl.leiden'
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
95 sa.tl.leiden(
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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96 adata,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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97 resolution = $method.resolution,
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98 objective_function = '$method.objective_function',
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99 min_cluster_size = $method.min_cluster_size,
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100 n_iterations = $method.n_iterations,
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101 random_state = $method.random_state,
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102 key_added = '$method.key_added',
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103 weighted = $method.weighted,
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104 inplace = True
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105 )
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106
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107 #else if $method.method == 'tl.kmeans'
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108 sa.tl.kmeans(
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109 adata,
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110 n_clusters = $method.n_clusters,
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111 n_iterations = $method.n_iterations,
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112 random_state = $method.random_state,
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113 use_rep = '$method.use_rep',
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114 key_added = '$method.key_added'
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115 )
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116
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117 #else if $method.method == 'tl.aggregate_X'
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118 sa.tl.aggregate_X(
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119 adata,
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120 #if $method.groupby != ''
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121 groupby = '$method.groupby',
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122 #end if
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123 normalize = '$method.normalize'
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124 )
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125
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126 #else if $method.method == 'tl.aggregate_cells'
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127 sa.tl.aggregate_cells(
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128 adata,
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129 use_rep = '$method.use_rep',
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130 #if $method.target_num_cells
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131 target_num_cells = $method.target_num_cells,
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132 #end if
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133 min_cluster_size = $method.min_cluster_size,
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134 random_state = $method.random_state,
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135 key_added = '$method.key_added',
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136 inplace = True
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137 )
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138 #end if
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139
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140 @CMD_anndata_write_outputs@
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141 ]]></configfile>
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142 </configfiles>
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143 <inputs>
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144 <conditional name="method">
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145 <param name="method" type="select" label="Dimension reduction and Clustering">
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146 <option value="tl.spectral">Perform dimension reduction using Laplacian Eigenmap, using 'tl.spectral'</option>
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147 <option value="tl.umap">Compute Umap, using 'tl.umap'</option>
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148 <option value="pp.knn">Compute a neighborhood graph of observations, using 'pp.knn'</option>
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149 <option value="tl.leiden">Cluster cells into subgroups, using 'tl.leiden'</option>
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150 <option value="tl.kmeans">Cluster cells into subgroups using the K-means algorithm, using 'tl.kmeans'</option>
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151 <option value="tl.dbscan">Cluster cells into subgroups using the DBSCAN algorithm, using 'tl.dbscan'</option>
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152 <option value="tl.hdbscan">Cluster cells into subgroups using the HDBSCAN algorithm, using 'tl.hdbscan'</option>
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153 <option value="tl.aggregate_X">Aggregate values in adata.X in a row-wise fashion, using 'tl.aggregate_X'</option>
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154 <option value="tl.aggregate_cells">Aggregate cells into pseudo-cells, using 'tl.aggregate_cells'</option>
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155 </param>
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156 <when value="tl.spectral">
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157 <expand macro="inputs_anndata"/>
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158 <expand macro="param_n_comps"/>
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159 <param argument="features" type="data" format="txt" optional="true" label="Text file indicating features to keep. Each line contains only word (True/False)." help="True means that the feature is kept. False means the feature is removed"/>
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160 <expand macro="param_random_state"/>
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161 <param argument="sample_size" type="float" min="0" max="1" optional="true" label="Approximate the embedding using the Nystrom algorithm by selecting a subset of cells" help="Using this only when the number of cells is too large, e.g. &gt; 10,000,000, or the `distance_metric` is “jaccard”"/>
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162 <param argument="chunk_size" type="integer" value="20000" label="chunk size"/>
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163 <param argument="distance_metric" type="select" label="distance metric: “jaccard”, “cosine“">
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164 <option value="jaccard">jaccard</option>
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165 <option value="cosine">cosine</option>
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166 </param>
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167 <param argument="weighted_by_sd" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to weight the result eigenvectors by the square root of eigenvalues"/>
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168 </when>
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169 <when value="tl.umap">
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170 <expand macro="inputs_anndata"/>
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171 <param argument="n_comps" type="integer" value="2" label="Number of dimensions of embedding"/>
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172 <param argument="use_dims" type="text" optional="true" label="Use these dimensions in `use_rep`" help="comma separated list of dimensions">
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173 <expand macro="sanitize_query"/>
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174 </param>
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175 <expand macro="param_use_rep"/>
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176 <expand macro="param_key_added" key_added="umap"/>
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177 <expand macro="param_random_state"/>
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178 </when>
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179 <when value="pp.knn">
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180 <expand macro="inputs_anndata"/>
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181 <param argument="n_neighbors" type="integer" value="50" label="The number of nearest neighbors to be searched"/>
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182 <param argument="use_dims" type="text" value="" optional="true" label="The dimensions used for computation">
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183 <expand macro="sanitize_query"/>
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184 </param>
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185 <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/>
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186 <param argument="algorithm" type="select" label="Choose method">
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187 <option value="kdtree" selected="true">'kdtree': use the kdtree algorithm to find the nearest neighbors</option>
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188 <option value="hora">'hora': use the HNSW algorithm to find the approximate nearest neighbors</option>
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189 <option value="pynndescent">'pynndescent': use the pynndescent algorithm to find the approximate nearest neighbors</option>
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190 </param>
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191 <param argument="random_state" type="integer" value="0" label="Random seed for approximate nearest neighbor search"/>
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192 </when>
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193 <when value="tl.leiden">
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194 <expand macro="inputs_anndata"/>
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195 <param argument="resolution" type="float" value="1" label="Parameter value controlling the coarseness of the clustering" help="Higher values lead to more clusters"/>
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196 <param argument="objective_function" type="select" label="Whether to use the Constant Potts Model (CPM) or modularity">
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197 <option value="CPM">CPM</option>
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198 <option value="modularity">modularity</option>
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199 <option value="RBConfiguration">RBConfiguration</option>
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200 </param>
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201 <param argument="min_cluster_size" type="integer" value="5" label="The minimum size of clusters"/>
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202 <expand macro="param_n_iterations"/>
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203 <expand macro="param_random_state"/>
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204 <expand macro="param_key_added" key_added="leiden"/>
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205 <param argument="weighted" type="boolean" truevalue="True" falsevalue="False" label="Whether to use the edge weights in the graph"/>
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206 </when>
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207 <when value="tl.kmeans">
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208 <expand macro="inputs_anndata"/>
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209 <param argument="n_clusters" type="integer" value="5" label="Number of clusters to return"/>
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210 <expand macro="param_n_iterations"/>
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211 <expand macro="param_random_state"/>
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212 <expand macro="param_use_rep"/>
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213 <expand macro="param_key_added" key_added="kmeans"/>
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214 </when>
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215 <when value="tl.dbscan">
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216 <expand macro="inputs_anndata"/>
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217 <param argument="eps" type="float" value="0.5" label=" The maximum distance between two samples for one to be considered as in the neighborhood of the other" help="This is not a maximum bound on the distances of points within a cluster. This is the most important DBSCAN parameter to choose appropriately for your data set and distance function."/>
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218 <param argument="min_samples" type="integer" value="5" label="The number of samples (or total weight) in a neighborhood for a point to be considered as a core point."/>
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219 <param argument="leaf_size" type="integer" value="30" label="Leaf size passed to BallTree or cKDTree" help="This can affect the speed of the construction and query, as well as the memory required to store the tree."/>
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220 <expand macro="param_use_rep"/>
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221 <expand macro="param_key_added" key_added="dbscan"/>
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222 </when>
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223 <when value="tl.hdbscan">
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224 <expand macro="inputs_anndata"/>
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225 <param argument="min_cluster_size" type="integer" value="5" label="The minimum size of clusters"/>
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226 <param argument="min_samples" type="integer" value="" optional="true" label="The number of samples in a neighbourhood for a point to be considered a core point"/>
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227 <param argument="cluster_selection_epsilon" type="float" value="0.0" label="A distance threshold. Clusters below this value will be merged"/>
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228 <param argument="alpha" type="float" value="1.0" label="A distance scaling parameter as used in robust single linkage"/>
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229 <param argument="cluster_selection_method" type="select" label="The method used to select clusters from the condensed tree">
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230 <option value="eom">Excess of Mass algorithm to find the most persistent clusters</option>
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231 <option value="leaf">Select the clusters at the leaves of the tree - this provides the most fine grained and homogeneous clusters</option>
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232 </param>
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233 <expand macro="param_random_state"/>
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234 <expand macro="param_use_rep"/>
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235 <expand macro="param_key_added" key_added="hdbscan"/>
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236 </when>
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237 <when value="tl.aggregate_X">
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238 <expand macro="inputs_anndata"/>
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239 <expand macro="param_groupby"/>
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240 <param argument="normalize" type="select" optional="true" label="normalization method">
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241 <option value="RPM">RPM</option>
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242 <option value="RPKM">RPKM</option>
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243 </param>
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244 </when>
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245 <when value="tl.aggregate_cells">
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246 <expand macro="inputs_anndata"/>
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247 <expand macro="param_use_rep"/>
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248 <param argument="target_num_cells" type="integer" value="" optional="true" label="target_num_cells" help="If None, `target_num_cells = num_cells / min_cluster_size`"/>
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249 <param argument="min_cluster_size" type="integer" value="50" label="The minimum size of clusters"/>
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250 <expand macro="param_random_state"/>
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251 <expand macro="param_key_added" key_added="pseudo_cell"/>
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252 </when>
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253 </conditional>
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254 <expand macro="inputs_common_advanced"/>
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255 </inputs>
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256 <outputs>
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257 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
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258 <data name="hidden_output" format="txt" label="Log file">
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259 <filter>advanced_common['show_log']</filter>
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260 </data>
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261 <data name="diff_peaks" format="tabular" from_work_dir="differential_peaks.tsv" label="${tool.name} on ${on_string}: Differential peaks">
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262 <filter>method['method'] and 'tl.diff_test' in method['method']</filter>
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263 </data>
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264 </outputs>
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265 <tests>
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266 <test expect_num_outputs="2">
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267 <!-- tl.spectral -->
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268 <conditional name="method">
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269 <param name="method" value="tl.spectral"/>
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270 <param name="adata" location="https://zenodo.org/records/11199963/files/pp.select_features.pbmc_500_chr21.h5ad"/>
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271 <param name="n_comps" value="30"/>
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272 <param name="random_state" value="0"/>
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273 <param name="chunk_size" value="20000"/>
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274 <param name="distance_metric" value="jaccard"/>
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275 <param name="weighted_by_sd" value="True"/>
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276 </conditional>
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277 <section name="advanced_common">
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278 <param name="show_log" value="true"/>
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279 </section>
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280 <output name="hidden_output">
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281 <assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
282 <has_text_matching expression="sa.tl.spectral"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
283 <has_text_matching expression="random_state = 0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
284 <has_text_matching expression="n_comps = 30"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
285 <has_text_matching expression="chunk_size = 20000"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
286 <has_text_matching expression="distance_metric = 'jaccard'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
287 <has_text_matching expression="weighted_by_sd = True"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
288 </assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
289 </output>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
290 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
291 </test>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
292 <test expect_num_outputs="2">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
293 <!-- tl.umap -->
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
294 <conditional name="method">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
295 <param name="method" value="tl.umap"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
296 <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
297 <param name="n_comps" value="2"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
298 <param name="use_rep" value="X_spectral"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
299 <param name="key_added" value="umap"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
300 <param name="random_state" value="0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
301 </conditional>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
302 <section name="advanced_common">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
303 <param name="show_log" value="true"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
304 </section>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
305 <output name="hidden_output">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
306 <assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
307 <has_text_matching expression="sa.tl.umap"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
308 <has_text_matching expression="n_comps = 2"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
309 <has_text_matching expression="use_rep = 'X_spectral'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
310 <has_text_matching expression="key_added = 'umap'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
311 <has_text_matching expression="random_state = 0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
312 </assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
313 </output>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
314 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.umap.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
315 </test>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
316 <test expect_num_outputs="2">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
317 <!-- pp.knn -->
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
318 <conditional name="method">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
319 <param name="method" value="pp.knn"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
320 <param name="adata" location="https://zenodo.org/records/11199963/files/tl.umap.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
321 <param name="n_neighbors" value="50"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
322 <param name="use_rep" value="X_spectral"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
323 <param name="method_" value="kdtree"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
324 <param name="inplace" value="True"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
325 <param name="random_state" value="0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
326 </conditional>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
327 <section name="advanced_common">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
328 <param name="show_log" value="true"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
329 </section>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
330 <output name="hidden_output">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
331 <assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
332 <has_text_matching expression="sa.pp.knn"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
333 <has_text_matching expression="n_neighbors = 50"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
334 <has_text_matching expression="use_rep = 'X_spectral'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
335 <has_text_matching expression="method = 'kdtree'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
336 <has_text_matching expression="inplace = True"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
337 <has_text_matching expression="random_state = 0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
338 </assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
339 </output>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
340 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/pp.knn.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
341 </test>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
342 <test expect_num_outputs="2">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
343 <!-- tl.leiden -->
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
344 <conditional name="method">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
345 <param name="method" value="tl.leiden"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
346 <param name="adata" location="https://zenodo.org/records/11199963/files/pp.knn.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
347 <param name="resolution" value="2"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
348 <param name="objective_function" value="modularity"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
349 <param name="min_cluster_size" value="3"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
350 <param name="n_iterations" value="-1"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
351 <param name="random_state" value="0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
352 <param name="key_added" value="leiden"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
353 <param name="weighted" value="False"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
354 </conditional>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
355 <section name="advanced_common">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
356 <param name="show_log" value="true"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
357 </section>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
358 <output name="hidden_output">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
359 <assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
360 <has_text_matching expression="sa.tl.leiden"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
361 <has_text_matching expression="resolution = 2"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
362 <has_text_matching expression="objective_function = 'modularity'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
363 <has_text_matching expression="min_cluster_size = 3"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
364 <has_text_matching expression="n_iterations = -1"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
365 <has_text_matching expression="random_state = 0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
366 <has_text_matching expression="key_added = 'leiden'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
367 <has_text_matching expression="weighted = False"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
368 </assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
369 </output>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
370 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.leiden.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
371 </test>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
372 <test expect_num_outputs="2">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
373 <!-- tl.kmeans -->
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
374 <conditional name="method">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
375 <param name="method" value="tl.kmeans"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
376 <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
377 <param name="n_iterations" value="-1"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
378 <param name="random_state" value="0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
379 <param name="use_rep" value="X_spectral"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
380 <param name="key_added" value="kmeans"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
381 </conditional>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
382 <section name="advanced_common">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
383 <param name="show_log" value="true"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
384 </section>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
385 <output name="hidden_output">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
386 <assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
387 <has_text_matching expression="sa.tl.kmeans"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
388 <has_text_matching expression="n_iterations = -1"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
389 <has_text_matching expression="random_state = 0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
390 <has_text_matching expression="use_rep = 'X_spectral'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
391 <has_text_matching expression="key_added = 'kmeans'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
392 </assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
393 </output>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
394 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.kmeans.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
395 </test>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
396 <test expect_num_outputs="2">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
397 <!-- tl.dbscan -->
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
398 <conditional name="method">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
399 <param name="method" value="tl.dbscan"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
400 <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
401 <param name="eps" value="0.5"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
402 <param name="min_samples" value="3"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
403 <param name="leaf_size" value="5"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
404 <param name="use_rep" value="X_spectral"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
405 <param name="key_added" value="dbscan"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
406 </conditional>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
407 <section name="advanced_common">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
408 <param name="show_log" value="true"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
409 </section>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
410 <output name="hidden_output">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
411 <assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
412 <has_text_matching expression="sa.tl.dbscan"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
413 <has_text_matching expression="eps = 0.5"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
414 <has_text_matching expression="min_samples = 3"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
415 <has_text_matching expression="leaf_size = 5"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
416 <has_text_matching expression="use_rep = 'X_spectral'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
417 <has_text_matching expression="key_added = 'dbscan'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
418 </assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
419 </output>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
420 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.dbscan.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
421 </test>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
422 <test expect_num_outputs="2">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
423 <!-- tl.hdbscan -->
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
424 <conditional name="method">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
425 <param name="method" value="tl.hdbscan"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
426 <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
427 <param name="min_cluster_size" value="3"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
428 <param name="min_samples" value="3"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
429 <param name="cluster_selection_method" value="eom"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
430 <param name="random_state" value="0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
431 <param name="use_rep" value="X_spectral"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
432 <param name="key_added" value="hdbscan"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
433 </conditional>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
434 <section name="advanced_common">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
435 <param name="show_log" value="true"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
436 </section>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
437 <output name="hidden_output">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
438 <assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
439 <has_text_matching expression="sa.tl.hdbscan"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
440 <has_text_matching expression="min_cluster_size = 3"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
441 <has_text_matching expression="min_samples = 3"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
442 <has_text_matching expression="cluster_selection_method = 'eom'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
443 <has_text_matching expression="random_state = 0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
444 <has_text_matching expression="use_rep = 'X_spectral'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
445 <has_text_matching expression="key_added = 'hdbscan'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
446 </assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
447 </output>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
448 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.hdbscan.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
449 </test>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
450 <test expect_num_outputs="2">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
451 <!-- tl.aggregate_X -->
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
452 <conditional name="method">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
453 <param name="method" value="tl.aggregate_X"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
454 <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
455 <param name="normalize" value="RPKM"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
456 </conditional>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
457 <section name="advanced_common">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
458 <param name="show_log" value="true"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
459 </section>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
460 <output name="hidden_output">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
461 <assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
462 <has_text_matching expression="sa.tl.aggregate_X"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
463 <has_text_matching expression="normalize = 'RPKM'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
464 </assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
465 </output>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
466 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.aggregate_X.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
467 </test>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
468 <test expect_num_outputs="2">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
469 <!-- tl.aggregate_cells -->
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
470 <conditional name="method">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
471 <param name="method" value="tl.aggregate_cells"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
472 <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
473 <param name="use_rep" value="X_spectral"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
474 <param name="target_num_cells" value="5"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
475 <param name="min_cluster_size" value="3"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
476 <param name="random_state" value="0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
477 <param name="key_added" value="pseudo_cell"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
478 </conditional>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
479 <section name="advanced_common">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
480 <param name="show_log" value="true"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
481 </section>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
482 <output name="hidden_output">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
483 <assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
484 <has_text_matching expression="sa.tl.aggregate_cells"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
485 <has_text_matching expression="use_rep = 'X_spectral'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
486 <has_text_matching expression="target_num_cells = 5"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
487 <has_text_matching expression="min_cluster_size = 3"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
488 <has_text_matching expression="random_state = 0"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
489 <has_text_matching expression="key_added = 'pseudo_cell'"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
490 </assert_contents>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
491 </output>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
492 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.aggregate_cells.pbmc_500_chr21.h5ad"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
493 </test>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
494 </tests>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
495 <help><![CDATA[
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
496 Perform dimension reduction using Laplacian Eigenmap, using `tl.spectral`
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
497 =========================================================================
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
498
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
499 Perform dimension reduction using Laplacian Eigenmaps.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
500
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
501 Convert the cell-by-feature count matrix into lower dimensional representations using the spectrum of the normalized graph Laplacian defined by pairwise similarity between cells. This function utilizes the matrix-free spectral embedding algorithm to compute the embedding when `distance_metric` is “cosine”, which scales linearly with the number of cells. For other types of similarity metrics, the time and space complexity scale quadratically with the number of cells.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
502
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
503 More details on the `SnapATAC2 documentation
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
504 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.spectral.html>`__
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
505
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
506 Compute Umap, using `tl.umap`
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
507 =============================
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
508
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
509 Compute Umap
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
510
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
511 More details on the `SnapATAC2 documentation
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
512 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.umap.html>`__
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
513
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
514 Compute a neighborhood graph of observations, using `pp.knn`
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
515 ============================================================
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
516
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
517 Compute a neighborhood graph of observations.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
518
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
519 Computes a neighborhood graph of observations stored in adata using the method specified by method. The distance metric used is Euclidean.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
520
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
521 More details on the `SnapATAC2 documentation
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
522 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.knn.html>`__
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
523
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
524 Cluster cells into subgroups, using `tl.leiden`
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
525 ===============================================
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
526
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
527 Cluster cells into subgroups.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
528
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
529 Cluster cells using the Leiden algorithm, an improved version of the Louvain algorithm. It has been proposed for single-cell analysis by. This requires having ran `knn`.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
530
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
531 More details on the `SnapATAC2 documentation
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
532 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.leiden.html>`__
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
533
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
534 Cluster cells into subgroups using the K-means algorithm, using `tl.kmeans`
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
535 ===========================================================================
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
536
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
537 Cluster cells into subgroups using the K-means algorithm, a classical algorithm in data mining.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
538
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
539 More details on the `SnapATAC2 documentation
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
540 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.kmeans.html>`__
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
541
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
542 Cluster cells into subgroups using the DBSCAN algorithm, using `tl.dbscan`
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
543 ==========================================================================
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
544
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
545 Cluster cells into subgroups using the DBSCAN algorithm.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
546
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
547 More details on the `SnapATAC2 documentation
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
548 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.dbscan.html>`__
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
549
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
550 Cluster cells into subgroups using the HDBSCAN algorithm, using `tl.hdbscan`
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
551 ============================================================================
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
552
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
553 Cluster cells into subgroups using the HDBSCAN algorithm.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
554
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
555 More details on the `SnapATAC2 documentation
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
556 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.hdbscan.html>`__
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
557
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
558 Aggregate values in adata.X in a row-wise fashion, using `tl.aggregate_X`
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
559 =========================================================================
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
560
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
561 Aggregate values in adata.X in a row-wise fashion.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
562
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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563 Aggregate values in adata.X in a row-wise fashion. This is used to compute RPKM or RPM values stratified by user-provided groupings.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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564
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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565 More details on the `SnapATAC2 documentation
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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566 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.aggregate_X.html>`__
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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567
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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568 Aggregate cells into pseudo-cells, using `tl.aggregate_cells`
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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569 =============================================================
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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570
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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571 Aggregate cells into pseudo-cells.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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572
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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573 Aggregate cells into pseudo-cells by iterative clustering.
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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574
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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575 More details on the `SnapATAC2 documentation
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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576 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.aggregate_cells.html>`__
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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577 ]]></help>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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578 <expand macro="citations"/>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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579 </tool>