Mercurial > repos > ebi-gxa > scanpy_normalise_data

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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 ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:42:20 +0000
parents 4bbb2179521c
children
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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3 <description>to make all cells having the same total expression</description>
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4 <macros>
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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[
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9 ln -s '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-normalise-data
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11 #if not $settings.default
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12 #if not $settings.log_transform
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13 ${settings.log_transform}
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14 #end if
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15 #if $settings.scale_factor
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16 --normalize-to '${settings.scale_factor}'
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17 #end if
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18 #if $settings.key_added
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19 --key-added '${settings.key_added}'
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20 #end if
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21 #if $settings.exclude.exclude_highly_expressed
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22 --exclude-highly-expressed --max-fraction '${settings.exclude.max_fraction}'
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23 #end if
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24 #end if
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25 @INPUT_OPTS@
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26 @OUTPUT_OPTS@
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27 @SAVE_MATRIX_OPTS@
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28 @EXPORT_MTX_OPTS@
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29 ]]></command>
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31 <inputs>
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32 <expand macro="input_object_params"/>
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33 <expand macro="output_object_params"/>
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34 <expand macro="export_mtx_params"/>
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35 <expand macro="save_matrix_params"/>
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36 <conditional name="settings">
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37 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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38 <when value="true"/>
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39 <when value="false">
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40 <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0"
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41 label="Target number to normalise to" help="Aimed counts per cell after normalisation."/>
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42 <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" checked="True"
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43 label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/>
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44 <conditional name="exclude">
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45 <param name="exclude_highly_expressed" argument="--exclude-highly-expressed" type="boolean" checked="False"
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46 label="Exclude highly expressed genes?" help="Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell. A gene is considered highly expressed, if it has more than max_fraction of the total counts in at least one cell. The not-excluded genes will sum up to the number specified by --normalize-to."/>
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47 <when value="true">
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48 <param name="max_fraction" argument="--max-fraction" type="float" value="0.05" min="0" max="1"
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49 label="Consider cells as highly expressed that have more counts than max_fraction of the original total counts in at least one cell." />
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50 </when>
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51 </conditional>
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52 <param name="layers" argument="--layers" type="text" optional="true"
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53 label="Comma-separated list of layers to normalize. Set to 'all' to normalize all layers."/>
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54 <param name="layer_norm" type="select" label="How to normalise layers" help="If None, after normalization, for each layer in layers each cell has a total count equal to the median of the counts_per_cell before normalization of the layer. If 'after', for each layer in layers each cell has a total count equal to the value of --normalize-to. If 'X', for each layer in layers each cell has a total count equal to the median of total counts for observations (cells) of adata.X before normalization." >
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55 <option value="" selected="true">None</option>
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56 <option value="X">X</option>
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57 <option value="after">after</option>
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58 </param>
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59
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60 <param name="key_added" argument="--key-added" type="text" optional="true"
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61 label="Name of the field in adata.obs where the normalization factor is stored. Default: don't store."/>
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62 </when>
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63 </conditional>
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64 </inputs>
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66 <outputs>
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67 <expand macro="output_data_obj" description="Normalised data"/>
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68 <expand macro="export_mtx_outputs"/>
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69 </outputs>
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70
1dda36e73482 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 <tests>
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72 <test>
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73 <param name="input_obj_file" value="filter_genes.h5"/>
1dda36e73482 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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74 <param name="input_format" value="anndata"/>
1dda36e73482 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 <param name="output_format" value="anndata"/>
1dda36e73482 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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76 <param name="scale_factor" value="1e4"/>
1dda36e73482 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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77 <param name="save_raw" value="false"/>
27
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78 <output name="output_h5" ftype="h5">
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79 <assert_contents>
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80 <has_h5_keys keys="var/n_cells_by_counts"/>
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81 </assert_contents>
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82 </output>
0
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83 </test>
1dda36e73482 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 </tests>
1dda36e73482 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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85
1dda36e73482 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><![CDATA[
1
e541f264fad2 "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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87 =============================================================
e541f264fad2 "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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88 Normalise total counts per cell (`scanpy.pp.normalize_total`)
e541f264fad2 "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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89 =============================================================
0
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90
1
e541f264fad2 "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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91 Normalise each cell by total counts over all genes (excluding top expressed
e541f264fad2 "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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92 genes if so required), so that every cell has the same total count after
e541f264fad2 "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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93 normalisation.
0
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94
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95 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
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96
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97 @HELP@
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98
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99 @VERSION_HISTORY@
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100 ]]></help>
1dda36e73482 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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101 <expand macro="citations"/>
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102 </tool>