Mercurial > repos > ebi-gxa > scanpy_find_variable_genes

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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 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
author ebi-gxa
date Wed, 15 May 2024 09:39:42 +0000
parents 2bc42a6f092b
children
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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@+galaxy1" profile="@PROFILE@">
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3 <description>based on normalised dispersion of expression</description>
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4 <macros>
1
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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 '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-find-variable-genes
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11 --flavor '${flavor}'
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12 #if $min_mean
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13 --mean-limits ${min_mean} ${max_mean}
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14 #end if
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15 #if $min_disp
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16 --disp-limits ${min_disp} ${max_disp}
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17 #end if
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18 #if $n_top_gene
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19 --n-top-genes ${n_top_gene}
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20 #end if
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21 #if $span
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22 --span ${span}
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23 #end if
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24 --n-bins '${n_bin}'
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25 ${filter}
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26 #if $batch_key
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27 --batch-key ${batch_key}
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28 #end if
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29 #if $never_hvg
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30 --never-hv-genes-file '${never_hvg}'
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31 #end if
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32 #if $always_hvg
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33 --always-hv-genes-file '${always_hvg}'
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34 #end if
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35 @INPUT_OPTS@
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36 @OUTPUT_OPTS@
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37 ]]></command>
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38
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39 <inputs>
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40 <expand macro="input_object_params"/>
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41 <expand macro="output_object_params"/>
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42 <param name="flavor" argument="--flavor" type="select" label="Flavor of computing normalised dispersion">
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43 <option value="seurat" selected="true">Seurat</option>
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44 <option value="cell_ranger">Cell-ranger</option>
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45 <option value="seurat_v3" selected="true">Seurat V3</option>
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46 </param>
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47 <param name="min_mean" argument="--min-mean" type="float" min="0" value="0.0125" optional="true"
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48 label="Min value for normalised mean expression (in log1p scale), ignored if flavor='seurat_v3'"/>
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49 <param name="max_mean" argument="--max-mean" type="float" min="0" value="3" optional="true"
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50 label="Max value for normalised mean expresssion (in log1p scale), Ignored if flavor='seurat_v3'"/>
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51 <param name="min_disp" argument="--min-disp" type="float" min="0" value="0.5" optional="true"
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52 label="Min value for dispersion of expression, ignored if flavor='seurat_v3'"/>
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53 <param name="max_disp" argument="--max-disp" type="float" min="0" value="50" optional="true"
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54 label="Max value for dispersion of expresssion, ignored if flavor='seurat_v3'"/>
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55 <param name="n_top_gene" argument="--n-top-genes" type="integer" value="2000" optional="true"
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56 label="Number of top variable genes to keep, mandatory if flavor='seurat_v3'"/>
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57 <param name="span" argument="--span" type="float" min="0" max="1" value="0.3" optional="true"
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58 label="The fraction of the data (cells) used when estimating the variance in the loess model fit if flavor='seurat_v3'"/>
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59 <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/>
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60 <param name="filter" argument="--subset" type="boolean" truevalue="--subset" falsevalue="" checked="false"
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61 label="Remove genes not marked as highly variable" help="When set, inplace subset to highly-variable genes, otherwise only flag highly-variable genes."/>
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62 <param name="batch_key" argument="--batch-key" type="text" label="Batch key" optional="true" help="If specified, highly-variable genes are selected within each batch separately and merged. This simple process avoids the selection of batch-specific genes and acts as a lightweight batch correction method. For all flavors, genes are first sorted by how many batches they are a HVG. For dispersion-based flavors ties are broken by normalized dispersion. If flavor = 'seurat_v3', ties are broken by the median (across batches) rank based on within-batch normalized variance."/>
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63 <param name="never_hvg" argument="--never-hv-genes-file" optional="true" type="data" label="Genes that should never be HVGs" help="Provide a file, one gene identifier per line, with genes that should never be active as HVGs. This simply makes sure that the boolean value for HVGs is false for all these genes after computing HVGs"/>
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64 <param name="always_hvg" argument="--always-hv-genes-file" optional="true" type="data" label="Genes that should never be HVGs" help="Provide a file, one gene identifier per line, with genes that should always be active as HVGs. This simply makes sure that the boolean value for HVGs is true for all these genes after computing HVGs"/>
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65 </inputs>
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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66
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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67 <outputs>
5
cb007db0857d 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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68 <expand macro="output_data_obj" description="Variable genes"/>
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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69 </outputs>
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
ebi-gxa
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71 <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
ebi-gxa
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72 <test>
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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73 <param name="input_obj_file" value="normalise_data.h5"/>
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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74 <param name="input_format" value="anndata"/>
305d0cbe0ffd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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75 <param name="output_format" value="anndata"/>
305d0cbe0ffd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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76 <param name="flavor" value="seurat"/>
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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77 <param name="n_bin" value="20"/>
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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78 <param name="min_mean" 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"
ebi-gxa
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79 <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"
ebi-gxa
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80 <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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81 <param name="max_disp" value="1e9"/>
27
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82 <output name="output_h5" ftype="h5">
2bc42a6f092b planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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83 <assert_contents>
2bc42a6f092b planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
ebi-gxa
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84 <has_h5_keys keys="uns/hvg"/>
2bc42a6f092b planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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85 </assert_contents>
2bc42a6f092b planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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86 </output>
0
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87 </test>
28
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88 <test>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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89 <param name="input_obj_file" value="normalise_data.h5"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
ebi-gxa
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90 <param name="never_hvg" value="never_hvg.txt"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
ebi-gxa
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91 <param name="always_hvg" value="always_hvg.txt"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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92 <param name="input_format" value="anndata"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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93 <param name="output_format" value="anndata"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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94 <param name="flavor" value="seurat"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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95 <param name="n_bin" value="20"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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96 <param name="min_mean" value="0.0125"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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97 <param name="max_mean" value="3"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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98 <param name="min_disp" value="0.5"/>
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99 <param name="max_disp" value="1e9"/>
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100 <output name="output_h5" ftype="h5">
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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101 <assert_contents>
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102 <has_h5_keys keys="uns/hvg"/>
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103 </assert_contents>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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104 </output>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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105 </test>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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106 <test>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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107 <param name="input_obj_file" value="normalise_data.h5"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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108 <param name="never_hvg" value="never_hvg.txt"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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109 <param name="input_format" value="anndata"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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110 <param name="output_format" value="anndata"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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111 <param name="flavor" value="seurat"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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112 <param name="n_bin" value="20"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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113 <param name="min_mean" value="0.0125"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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114 <param name="max_mean" value="3"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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115 <param name="min_disp" value="0.5"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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116 <param name="max_disp" value="1e9"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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117 <output name="output_h5" ftype="h5">
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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118 <assert_contents>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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119 <has_h5_keys keys="uns/hvg"/>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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120 </assert_contents>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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121 </output>
64dd8bb151e1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
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122 </test>
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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123 </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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124
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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125 <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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126 ==============================================================
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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127 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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128 ==============================================================
0
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129
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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130 Depending on `flavor`, this reproduces the R-implementations of Seurat or Cell Ranger.
0
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131
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132 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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133 deviation of the dispersions for genes falling into a given bin for mean
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134 expression of genes. This means that for each bin of mean expression, highly
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135 variable genes are selected.
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136
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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137 @HELP@
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138
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139 @VERSION_HISTORY@
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140 ]]></help>
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141 <expand macro="citations">
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142 <citation type="doi">10.1038/nbt.3192</citation>
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143 <citation type="doi">10.1038/ncomms14049</citation>
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144 </expand>
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145 </tool>