Mercurial > repos > ebi-gxa > seurat_find_neighbours

annotate seurat_find_neighbours.xml @ 3:ab622ffd7c7f draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:48:19 +0000
parents bba8b14264c2
children 99d628557c47
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1 <tool id="seurat_find_neighbours" name="Seurat FindNeighbours" version="@SEURAT_VERSION@+galaxy0">
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2 <description>constructs a Shared Nearest Neighbor (SNN) Graph</description>
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3 <macros>
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4 <import>seurat_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 seurat-find-neighbours.R
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10 @INPUT_OBJECT@
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11 $distance_matrix
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12 #if $k_param
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13 --k-param '$k_param'
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14 #end if
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15 $compute_snn
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16 #if $prune_snn
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17 --prune-snn '$prune_snn'
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18 #end if
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19 #if $nn_method
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20 --nn-method '$nn_method'
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21 #end if
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22 #if $annoy_metric
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23 --annoy-metric '$annoy_metric'
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24 #end if
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25 #if $graph_name
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26 --graph-name '$graph_name'
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27 #end if
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28 #if $nn_eps and $nn_method == "rann"
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29 --nn-eps '$nn_eps'
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30 #end if
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31 $force_recalc
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32 #if $features_file
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33 --features '$features_file'
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34 #else if $features
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35 --features '$features'
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36 #end if
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37 #if $reduction
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38 --reduction '$reduction'
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39 #end if
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40 #if $dims
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41 --dims '$dims'
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42 #end if
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43 #if $assay
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44 --assay '$assay'
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45 #end if
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46 #if $do_plot
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47 $do_plot
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48 #end if
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49 @OUTPUT_OBJECT@
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50 ]]></command>
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51
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52 <inputs>
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53 <expand macro="input_object_params"/>
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54 <expand macro="output_object_params"/>
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55 <param label="Features" optional="true" name="features" argument="--features" type="text" help="Comma-separated list of genes to use for building SNN."/>
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56 <param label="Features file" optional="true" name="features_file" argument="--features" type="data" format="txt,tabular" help="Text file with one gene per line to use for building SNN. Overrides Features."/>
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57 <param label="Plot SNN on tSNE" optional="true" name="do_plot" argument="--do-plot" type="boolean" truevalue="--do-plot" checked="false" help="Plot SNN graph on tSNE coordinates"/>
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58 <param label="Reduction" optional="true" name="reduction" argument="--reduction" type="text" help="Reduction to use as input for building the SNN"/>
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59 <param label="Dimensions" optional="true" name="dims" argument="--dims" type="text" help="Dimensions of reduction to use as input. A comma-separated list of the dimensions to use in construction of the SNN graph (e.g. To use the first 5 PCs, pass 1,2,3,4,5)."/>
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60 <param label="Assay" optional="true" name="assay" argument="--assay" type="text" help="Assay to use in construction of SNN"/>
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61 <param label="Distance matrix" optional="true" name="distance_matrix" argument="--distance-matrix" type="boolean" truevalue="--distance-matrix" falsevalue="" checked="false" help="Boolean value of whether the provided matrix is a distance matrix; note, for objects of class dist, this parameter will be set automatically."/>
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62 <param label="k" optional="true" name="k_param" argument="--k-param" type="integer" help="Defines k for the k-nearest neighbor algorithm"/>
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63 <param label="Compute SNN" optional="true" name="compute_snn" argument="--compute-snn" type="boolean" truevalue="--compute-snn" falsevalue="" checked="false" help="Also compute the shared nearest neighbor graph"/>
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64 <param label="Prune SNN" optional="true" name="prune_snn" argument="--prune-snn" type="float" help="Sets the cutoff for acceptable Jaccard index when computing the neighborhood overlap for the SNN construction. Any edges with values less than or equal to this will be set to 0 and removed from the SNN graph. Essentially sets the strigency of pruning (0 --- no pruning, 1 --- prune everything)."/>
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65 <param label="NN method" optional="true" name="nn_method" argument="--nn-method" type="select" help="Method for nearest neighbor finding. Options include: rann (default), annoy">
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66 <option value="rann" selected="true">rann</option>
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67 <option value="annoy">annoy</option>
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68 </param>
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69 <param label="Annoy metric" optional="true" name="annoy_metric" argument="--annoy-metric" type="select" help="Distance metric for annoy. Options include: euclidean (default), cosine, manhattan, and hamming">
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70 <option value="euclidean" selected="true">Euclidean</option>
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71 <option value="cosine">Cosine</option>
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72 <option value="manhattan">Manhattan</option>
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73 <option value="hamming">Hamming</option>
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74 </param>
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75 <param label="Graph name" optional="true" name="graph_name" argument="--graph-name" type="text" help="Name of graph to use for the clustering algorithm."/>
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76 <param label="NN Error bound" optional="true" name="nn_eps" argument="--nn-eps" type="float" help="Error bound when performing nearest neighbor seach using RANN; default of 0.0 implies exact nearest neighbor search"/>
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77 <param label="Force recalc" optional="true" name="force_recalc" argument="--force-recalc" type="boolean" truevalue="--force-recalc" falsevalue="" checked="false" help="Force recalculation of SNN"/>
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78 </inputs>
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79
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80 <outputs>
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81 <expand macro="output_files"/>
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82 <data name="snn_on_tsne" format="pdf" from_work_dir="snn_on_tsne.pdf" label="${tool.name} on ${on_string}: SNN on tSNE Plot">
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83 <filter>do_plot</filter>
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84 </data>
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85 </outputs>
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86
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87 <tests>
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88 <test>
3
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89 <param name="rds_seurat_file" ftype="rdata" value="pca_seurat.rds"/>
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90 <param name="compute_snn" value="True" />
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91 <param name="reduction" value="pca" />
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92 <output name="rds_seurat_file" ftype="rdata" value="neighbours_seurat.rds" compare="sim_size" delta="10000000" />
0
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93 </test>
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94 </tests>
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95 <help><![CDATA[
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96 .. class:: infomark
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97
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98 **What it does**
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99
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100 Constructs a Shared Nearest Neighbor (SNN) Graph for a given dataset.
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101 We first determine the k-nearest neighbors of each cell. We use this knn graph
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102 to construct the SNN graph by calculating the neighborhood overlap (Jaccard index)
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103 between every cell and its k.param nearest neighbors.
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104
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105 @SEURAT_INTRO@
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106
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107 -----
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108
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109 **Inputs**
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110
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111 * Seurat RDS object. Probably the one produced by Seurat create object.
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112 * Subset names. A list of attributes to subset on, colon separated (:).
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113 * Low thresholds. A minimum value for each of the attributes set in subset names, again, colon separated (:). Optional.
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114 * High thresholds. A maximum value for each of the attributes set in subset names, again, colon separated (:). Optional.
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115 * Cells to use. A list of cell names/idenfifiers to filter positively by.
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116
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117 -----
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118
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119 **Outputs**
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120
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121 * Seurat RDS object filtered according to the inputs.
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122
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123 .. _Seurat: https://www.nature.com/articles/nbt.4096
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124 .. _Satija Lab: https://satijalab.org/seurat/
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125
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126 @VERSION_HISTORY@
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127
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128 ]]></help>
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129 <expand macro="citations" />
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130 </tool>