Mercurial > repos > ebi-gxa > scanpy_find_cluster

annotate scanpy-find-cluster.xml @ 16:5e68e130fafe draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
author ebi-gxa
date Thu, 17 Sep 2020 16:24:22 +0000
parents c46750e2e4a4
children b45b85d5c7ec
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ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <?xml version="1.0" encoding="utf-8"?>
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5e68e130fafe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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3 <description>based on community detection on KNN graph</description>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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4 <macros>
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5 <import>scanpy_macros2.xml</import>
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ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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6 </macros>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #from pathlib import Path
5e68e130fafe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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10 #if $settings.resolution_file
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11 #set resolution = Path($settings.resolution_file.__str__).read_text().strip()
5e68e130fafe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
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12 #elif $settings.resolution
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13 #set resolution = $settings.resolution.__str__.strip()
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14 #end if
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15
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16 ln -s '${input_obj_file}' input.h5 &&
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17 PYTHONIOENCODING=utf-8 scanpy-find-cluster
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18 ${method}
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19 #if $settings.default == "false"
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20 --neighbors-key '${settings.neighbors_key}'
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21 #if $settings.key_added
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22 #set key_added = $settings.key_added.replace('METHOD', $method.__str__)
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23 #if $resolution
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24 #set key_added = $key_added.replace('RESOLUTION', $resolution.__str__)
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25 #end if
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26 --key-added '${key_added}'
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27 #end if
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28 #if $resolution
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29 --resolution '$resolution'
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30 #end if
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31 #if $settings.layer
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32 --layer '${settings.layer}'
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33 #end if
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34 #if $settings.restrict_to
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35 --restrict-to '${settings.restrict_to}'
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36 #end if
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37 #if $settings.use_weights
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38 --use-weights
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39 #end if
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40 --random-state '${settings.random_seed}'
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41 ${settings.directed}
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42 #end if
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43 #if $output_cluster
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44 --export-cluster output.tsv
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45 #end if
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46 @INPUT_OPTS@
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47 @OUTPUT_OPTS@
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48 ]]></command>
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49
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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50 <inputs>
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51 <expand macro="input_object_params"/>
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52 <expand macro="output_object_params"/>
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53 <param name="output_cluster" type="boolean" checked="true" label="Output cluster in two column text format"/>
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54
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55 <param name="method" type="select" label="Clustering algorithm">
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56 <option value="louvain" selected="true">Louvain</option>
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57 <option value="leiden">Leiden</option>
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58 </param>
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59
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60 <conditional name="settings">
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61 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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62 <when value="true"/>
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63 <when value="false">
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64 <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text"
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65 label="Name of the slot that holds the KNN graph"/>
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66 <param name="layer" argument="--layer" value="" type="text"
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67 label="Key from adata.layers whose value will be used to perform tests on. (Default: use .X)"/>
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68 <param name="key_added" argument="--key-added" type="text" optional="true"
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69 label="Additional suffix to the name of the slot to save the calculated clustering" help="If included, the keyword 'METHOD' will be substituted with the value of the method setting and 'RESOLUTION' with the value of that field."/>
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70 <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0"
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71 label="Resolution, high value for more and smaller clusters"/>
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72 <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true"
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73 label="File with resolution, use with parameter iterator. Overrides the resolution setting"/>
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74 <param name="restrict_to" argument="--restrict-to" type="text" optional="true"
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75 label="Restrict clustering to certain sample categories"/>
0
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76 <param name="use_weights" argument="--use-weights" type="boolean" checked="false" label="Use weights from knn graph"/>
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77 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
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78 <param name="directed" argument="--directed" type="boolean" truevalue="--directed" falsevalue="--undirected" checked="true"
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79 label="Interpret the adjacency matrix as directed graph."/>
0
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80 </when>
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81 </conditional>
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82 </inputs>
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83
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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84 <outputs>
5
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85 <expand macro="output_data_obj" description="Clusters"/>
0
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86 <data name="output_txt" format="tsv" from_work_dir="output.tsv" label="${tool.name} on ${on_string}: Cluster table">
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87 <filter>output_cluster</filter>
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88 </data>
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89 </outputs>
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90
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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91 <tests>
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92 <test>
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93 <param name="input_obj_file" value="compute_graph.h5"/>
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94 <param name="input_format" value="anndata"/>
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95 <param name="output_format" value="anndata"/>
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96 <param name="output_txt" value="true"/>
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97 <param name="default" value="false"/>
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98 <param name="resolution" value="1.0"/>
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99 <param name="random_seed" value="0"/>
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100 <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/>
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101 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/>
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102 </test>
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103 </tests>
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104
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105 <help><![CDATA[
1
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106 ======================================================================
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107 Cluster cells into subgroups (`scanpy.tl.louvain`, `scanpy.tl.leiden`)
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108 ======================================================================
0
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109
1
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110 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the
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111 implementation of Traag et al, 2017, or the Leiden algorithm (Traag et al,
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112 2019). The Louvain algorithm has been proposed for single-cell analysis by
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113 Levine et al, 2015.
0
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114
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115 This requires to run `Scanpy ComputeGraph`, first.
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116
1
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117 It by default yields `louvain` or `leiden`, generated cluster label.
0
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118
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119 @HELP@
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120
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121 @VERSION_HISTORY@
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122 ]]></help>
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123 <expand macro="citations">
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124 <citation type="doi">10.1088/1742-5468/2008/10/P10008</citation>
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125 <citation type="doi">10.1016/j.cell.2015.05.047</citation>
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126 <citation type="doi">10.1038/s41598-019-41695-z</citation>
0
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127 <citation type="doi">10.5281/zenodo.35117</citation>
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128 </expand>
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129 </tool>