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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 13:13:49 +0000
parents a97c37e0309a
children 3a4564b9d685
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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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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[
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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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 #if $settings.save_raw
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25 --save-raw ${settings.save_raw}
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26 #end if
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27 #end if
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28 @INPUT_OPTS@
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29 @OUTPUT_OPTS@
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30 @EXPORT_MTX_OPTS@
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31 ]]></command>
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32
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33 <inputs>
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34 <expand macro="input_object_params"/>
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35 <expand macro="output_object_params"/>
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36 <expand macro="export_mtx_params"/>
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37 <conditional name="settings">
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38 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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39 <when value="true"/>
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40 <when value="false">
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41 <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0"
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42 label="Target number to normalise to" help="Aimed counts per cell after normalisation."/>
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43 <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" checked="True"
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44 label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/>
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45 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true"
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46 label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/>
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47 <conditional name="exclude">
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48 <param name="exclude_highly_expressed" argument="--exclude-highly-expressed" type="boolean" checked="False"
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49 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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50 <when value="true">
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51 <param name="max_fraction" argument="--max-fraction" type="float" value="0.05" min="0" max="1"
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52 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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53 </when>
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54 </conditional>
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55 <param name="layers" argument="--layers" type="text" optional="true"
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56 label="Comma-separated list of layers to normalize. Set to 'all' to normalize all layers."/>
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57 <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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58 <option value="" selected="true">None</option>
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59 <option value="X">X</option>
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60 <option value="after">after</option>
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61 </param>
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62
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63 <param name="key_added" argument="--key-added" type="text" optional="true"
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64 label="Name of the field in adata.obs where the normalization factor is stored. Default: don't store."/>
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65 </when>
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66 </conditional>
0
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67 </inputs>
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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68
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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69 <outputs>
6
9e42d8795385 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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70 <expand macro="output_data_obj" description="Normalised data"/>
0
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 <expand macro="export_mtx_outputs"/>
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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72 </outputs>
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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73
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 <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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75 <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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76 <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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77 <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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78 <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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79 <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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80 <param name="save_raw" value="false"/>
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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81 <output name="output_h5" file="normalise_data.h5" ftype="h5" compare="sim_size"/>
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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82 </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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83 </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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84
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 <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"
ebi-gxa
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86 =============================================================
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 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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88 =============================================================
0
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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89
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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90 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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91 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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92 normalisation.
0
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93
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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94 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
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95
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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96 @HELP@
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97
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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98 @VERSION_HISTORY@
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99 ]]></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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100 <expand macro="citations"/>
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 </tool>