Mercurial > repos > ebi-gxa > scanpy_find_cluster

annotate scanpy-find-cluster.xml @ 0:2cb836f82ddb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
author ebi-gxa
date Wed, 13 Mar 2019 11:49:57 -0400
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2cb836f82ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy1">
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3 <description>based on community detection on KNN graph</description>
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4 <macros>
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5 <import>scanpy_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-find-cluster.py
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11 -i input.h5
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12 -f '${input_format}'
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13 -o output.h5
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14 -F '${output_format}'
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15 #if $output_cluster
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16 --output-text-file output.tsv
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17 #end if
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18 #if $settings.default == "false"
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19 --flavor '${settings.flavor}'
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20 --key-added '${settings.key_added}'
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21 -s '${settings.random_seed}'
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22 #if $settings.flavor == "vtraag" and $settings.resolution_file
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23 --resolution \$( cat $settings.resolution_file )
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24 #elif $settings.flavor == "vtraag"
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25 --resolution '${settings.resolution}'
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26 #end if
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27 #if $settings.restrict_to
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28 --restrict-to '${settings.restrict_to}'
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29 #end if
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30 #if $settings.use_weights
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31 --use-weights
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32 #end if
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33 #end if
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34 ]]></command>
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35
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36 <inputs>
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37 <expand macro="input_object_params"/>
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38 <expand macro="output_object_params"/>
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39 <param name="output_cluster" type="boolean" checked="true" label="Output cluster in two column text format"/>
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40 <conditional name="settings">
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41 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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42 <when value="true"/>
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43 <when value="false">
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44 <param name="flavor" argument="--flavor" type="select" label="Use the indicated representation">
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45 <option value="vtraag" selected="true">vtraag</option>
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46 <option value="igraph">igraph</option>
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47 </param>
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48 <param name="resolution" argument="--resolution" type="float" value="1.0" label="Resolution, high value for more and smaller clusters"/>
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49 <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true" label="File with resolution, use with parameter iterator. Overrides the resolution setting"/>
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50 <param name="restrict_to" argument="--restrict-to" type="text" optional="true" label="Restrict clustering to certain sample categories"/>
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51 <param name="key_added" argument="--key-added" type="text" value="louvain" label="Key under which to add the cluster labels (do not change unless you know what you are doing)"/>
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52 <param name="use_weights" argument="--use-weights" type="boolean" checked="false" label="Use weights from knn graph"/>
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53 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
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54 </when>
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55 </conditional>
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56 </inputs>
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57
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58 <outputs>
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59 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Cluster object"/>
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60 <data name="output_txt" format="tsv" from_work_dir="output.tsv" label="${tool.name} on ${on_string}: Cluster table">
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61 <filter>output_cluster</filter>
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62 </data>
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63 </outputs>
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64
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65 <tests>
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66 <test>
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67 <param name="input_obj_file" value="compute_graph.h5"/>
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68 <param name="input_format" value="anndata"/>
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69 <param name="output_format" value="anndata"/>
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70 <param name="output_txt" value="true"/>
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71 <param name="default" value="false"/>
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72 <param name="flavor" value="vtraag"/>
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73 <param name="resolution" value="1.0"/>
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74 <param name="random_seed" value="0"/>
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75 <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/>
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76 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/>
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77 </test>
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78 </tests>
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79
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80 <help><![CDATA[
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81 ===========================================
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82 Cluster cells into subgroups (`tl.louvain`)
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83 ===========================================
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84
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85 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the implementation
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86 of Traag et al,2017. The Louvain algorithm has been proposed for single-cell
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87 analysis by Levine et al, 2015.
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88
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89 This requires to run `Scanpy ComputeGraph`, first.
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90
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91 It yields `louvain`, generated cluster label.
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92
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93 @HELP@
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94
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95 @VERSION_HISTORY@
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96 ]]></help>
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97 <expand macro="citations">
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98 <citation type="doi">10.1088/1742-5468/2008/10/P10008</citation>
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99 <citation type="doi">10.1016/j.cell.2015.05.047</citation>
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100 <citation type="doi">10.5281/zenodo.35117</citation>
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101 </expand>
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102 </tool>