Mercurial > repos > ebi-gxa > scanpy_find_variable_genes

annotate scanpy-find-variable-genes.xml @ 4:258e13397a8a 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 1d069e25584e436d7628694cb8853a15f1f85604
author ebi-gxa
date Wed, 20 Nov 2019 05:18:33 -0500
parents b089f4a55e6b
children cb007db0857d
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305d0cbe0ffd 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"?>
305d0cbe0ffd 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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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>
1
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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5 <import>scanpy_macros2.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[
305d0cbe0ffd 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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9 ln -s '${input_obj_file}' input.h5 &&
1
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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10 PYTHONIOENCODING=utf-8 scanpy-find-variable-genes
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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11 --flavor '${method.flavor}'
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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12 #if $method.flavor == 'seurat'
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13 --mean-limits ${method.min_mean} ${method.max_mean}
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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14 --disp-limits ${method.min_disp} ${method.max_disp}
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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15 #else
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16 --n-top-genes ${method.n_top_gene}
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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17 #end if
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18 --n-bins '${n_bin}'
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19 ${filter}
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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20 @INPUT_OPTS@
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21 @OUTPUT_OPTS@
0
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22 ]]></command>
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23
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24 <inputs>
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25 <expand macro="input_object_params"/>
305d0cbe0ffd 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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26 <expand macro="output_object_params"/>
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b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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27 <conditional name="method">
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28 <param name="flavor" argument="--flavor" type="select" label="Flavor of computing normalised dispersion">
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29 <option value="seurat" selected="true">Seurat</option>
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30 <option value="cell_ranger">Cell-ranger</option>
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31 </param>
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32 <when value="seurat">
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33 <param name="min_mean" argument="--min-mean" type="float" min="0" value="0.0125"
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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34 label="Min value for normalised mean expression (in log1p scale)"/>
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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35 <param name="max_mean" argument="--max-mean" type="float" min="0" value="3"
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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36 label="Max value for normalised mean expresssion (in log1p scale)"/>
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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37 <param name="min_disp" argument="--min-disp" type="float" min="0" value="0.5"
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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38 label="Min value for dispersion of expression"/>
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39 <param name="max_disp" argument="--max-disp" type="float" min="0" value="50"
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40 label="Max value for dispersion of expresssion"/>
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41 </when>
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42 <when value="cell_ranger">
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43 <param name="n_top_gene" argument="--n-top-genes" type="integer" value="2000"
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44 label="Number of top variable genes to keep"/>
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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45 </when>
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46 </conditional>
0
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47 <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/>
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48 <param name="filter" argument="--subset" type="boolean" truevalue="--subset" falsevalue="" checked="false"
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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49 label="Remove genes not marked as highly variable"/>
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50 </inputs>
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51
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52 <outputs>
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53 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Variable genes"/>
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54 </outputs>
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55
305d0cbe0ffd 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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56 <tests>
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57 <test>
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58 <param name="input_obj_file" value="normalise_data.h5"/>
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59 <param name="input_format" value="anndata"/>
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60 <param name="output_format" value="anndata"/>
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61 <param name="flavor" value="seurat"/>
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62 <param name="n_bin" value="20"/>
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63 <param name="min_mean" value="0.0125"/>
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64 <param name="max_mean" value="3"/>
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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65 <param name="min_disp" value="0.5"/>
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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66 <param name="max_disp" value="1e9"/>
0
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67 <output name="output_h5" file="find_variable_genes.h5" ftype="h5" compare="sim_size"/>
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68 </test>
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69 </tests>
305d0cbe0ffd 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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70
305d0cbe0ffd 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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71 <help><![CDATA[
1
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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72 ==============================================================
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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73 Mark highly variable genes (`scanpy.pp.highly_variable_genes`)
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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74 ==============================================================
0
305d0cbe0ffd 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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75
1
b089f4a55e6b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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76 Depending on `flavor`, this reproduces the R-implementations of Seurat or Cell Ranger.
0
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77
305d0cbe0ffd 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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78 The normalized dispersion is obtained by scaling with the mean and standard
305d0cbe0ffd 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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79 deviation of the dispersions for genes falling into a given bin for mean
305d0cbe0ffd 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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80 expression of genes. This means that for each bin of mean expression, highly
305d0cbe0ffd 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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81 variable genes are selected.
305d0cbe0ffd 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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82
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83 @HELP@
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84
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85 @VERSION_HISTORY@
305d0cbe0ffd 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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86 ]]></help>
305d0cbe0ffd 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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87 <expand macro="citations">
305d0cbe0ffd 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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88 <citation type="doi">10.1038/nbt.3192</citation>
305d0cbe0ffd 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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89 <citation type="doi">10.1038/ncomms14049</citation>
305d0cbe0ffd 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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90 </expand>
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91 </tool>