Mercurial > repos > ebi-gxa > scanpy_find_variable_genes

annotate scanpy-find-variable-genes.xml @ 0:4765cea381e3 draft

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author ebi-gxa
date Wed, 13 Mar 2019 11:51:42 -0400
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children 70840a50d3d2
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy0">
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3 <description>based on normalised dispersion of expression</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 '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-find-variable-genes.py -i input.h5
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11 -f '${input_format}'
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12 -o output.h5
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13 -F '${output_format}'
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14 --flavor '${flavor}'
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15 -b '${n_bin}'
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16 #if $parameters
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17 #set pars = ','.join([str($p['name']) for $p in $parameters])
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18 -p '${pars}'
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19 #set mins = ','.join([str($p['min']) for $p in $parameters])
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20 -l '${mins}'
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21 #set maxs = ','.join([str($p['max']) for $p in $parameters])
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22 -j '${maxs}'
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23 #end if
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24 #if $n_top_gene
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25 -n '${n_top_gene}'
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26 #end if
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27 ]]></command>
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28
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29 <inputs>
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30 <expand macro="input_object_params"/>
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31 <expand macro="output_object_params"/>
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32 <param name="flavor" argument="--flavor" type="select" value="seurat" label="Flavor of computing normalised dispersion">
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33 <option value="seurat">Seurat</option>
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34 <option value="cell_ranger">Cell-ranger</option>
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35 </param>
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36 <repeat name="parameters" min="1" title="Parameters used to find variable genes">
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37 <param name="name" type="select" label="Name of parameter to filter on">
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38 <option value="mean">Mean of expression</option>
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39 <option value="disp">Dispersion of expression</option>
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40 </param>
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41 <param name="min" type="float" value="0" label="Min value"/>
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42 <param name="max" type="float" value="1e9" label="Max value"/>
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43 </repeat>
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44 <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/>
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45 <param name="n_top_gene" argument="--n-top-genes" type="integer" optional="true" label="Number of top variable genes to keep"/>
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46 </inputs>
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47
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48 <outputs>
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49 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Variable genes"/>
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50 </outputs>
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51
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52 <tests>
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53 <test>
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54 <param name="input_obj_file" value="normalise_data.h5"/>
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55 <param name="input_format" value="anndata"/>
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56 <param name="output_format" value="anndata"/>
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57 <param name="flavor" value="seurat"/>
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58 <param name="n_bin" value="20"/>
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59 <repeat name="parameters">
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60 <param name="name" value="mean"/>
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61 <param name="min" value="0.0125"/>
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62 <param name="max" value="3"/>
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63 </repeat>
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64 <repeat name="parameters">
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65 <param name="name" value="disp"/>
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66 <param name="min" value="0.5"/>
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67 <param name="max" value="1e9"/>
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68 </repeat>
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69 <output name="output_h5" file="find_variable_genes.h5" ftype="h5" compare="sim_size"/>
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70 </test>
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71 </tests>
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72
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73 <help><![CDATA[
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74 ============================================================
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75 Extract highly variable genes (`pp.filter_genes_dispersion`)
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76 ============================================================
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77
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78 Depending on `flavor`, this reproduces the R-implementations of Seurat and Cell Ranger.
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79
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80 The normalized dispersion is obtained by scaling with the mean and standard
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81 deviation of the dispersions for genes falling into a given bin for mean
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82 expression of genes. This means that for each bin of mean expression, highly
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83 variable genes are selected.
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84
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85 @HELP@
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86
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87 @VERSION_HISTORY@
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88 ]]></help>
4765cea381e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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89 <expand macro="citations">
4765cea381e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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90 <citation type="doi">10.1038/nbt.3192</citation>
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91 <citation type="doi">10.1038/ncomms14049</citation>
4765cea381e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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92 </expand>
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93 </tool>