Mercurial > repos > ebi-gxa > scanpy_find_variable_genes

comparison scanpy-find-variable-genes.xml @ 28:64dd8bb151e1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
27:2bc42a6f092b 28:64dd8bb151e1
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>based on normalised dispersion of expression</description> 3 <description>based on normalised dispersion of expression</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
23 #end if 23 #end if
24 --n-bins '${n_bin}' 24 --n-bins '${n_bin}'
25 ${filter} 25 ${filter}
26 #if $batch_key 26 #if $batch_key
27 --batch-key ${batch_key} 27 --batch-key ${batch_key}
28 #end if
29 #if $never_hvg
30 --never-hv-genes-file '${never_hvg}'
31 #end if
32 #if $always_hvg
33 --always-hv-genes-file '${always_hvg}'
28 #end if 34 #end if
29 @INPUT_OPTS@ 35 @INPUT_OPTS@
30 @OUTPUT_OPTS@ 36 @OUTPUT_OPTS@
31 ]]></command> 37 ]]></command>
32 38
52 label="The fraction of the data (cells) used when estimating the variance in the loess model fit if flavor='seurat_v3'"/> 58 label="The fraction of the data (cells) used when estimating the variance in the loess model fit if flavor='seurat_v3'"/>
53 <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/> 59 <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/>
54 <param name="filter" argument="--subset" type="boolean" truevalue="--subset" falsevalue="" checked="false" 60 <param name="filter" argument="--subset" type="boolean" truevalue="--subset" falsevalue="" checked="false"
55 label="Remove genes not marked as highly variable" help="When set, inplace subset to highly-variable genes, otherwise only flag highly-variable genes."/> 61 label="Remove genes not marked as highly variable" help="When set, inplace subset to highly-variable genes, otherwise only flag highly-variable genes."/>
56 <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."/> 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."/>
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"/>
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"/>
57 </inputs> 65 </inputs>
58 66
59 <outputs> 67 <outputs>
60 <expand macro="output_data_obj" description="Variable genes"/> 68 <expand macro="output_data_obj" description="Variable genes"/>
61 </outputs> 69 </outputs>
62 70
63 <tests> 71 <tests>
64 <test> 72 <test>
65 <param name="input_obj_file" value="normalise_data.h5"/> 73 <param name="input_obj_file" value="normalise_data.h5"/>
74 <param name="input_format" value="anndata"/>
75 <param name="output_format" value="anndata"/>
76 <param name="flavor" value="seurat"/>
77 <param name="n_bin" value="20"/>
78 <param name="min_mean" value="0.0125"/>
79 <param name="max_mean" value="3"/>
80 <param name="min_disp" value="0.5"/>
81 <param name="max_disp" value="1e9"/>
82 <output name="output_h5" ftype="h5">
83 <assert_contents>
84 <has_h5_keys keys="uns/hvg"/>
85 </assert_contents>
86 </output>
87 </test>
88 <test>
89 <param name="input_obj_file" value="normalise_data.h5"/>
90 <param name="never_hvg" value="never_hvg.txt"/>
91 <param name="always_hvg" value="always_hvg.txt"/>
92 <param name="input_format" value="anndata"/>
93 <param name="output_format" value="anndata"/>
94 <param name="flavor" value="seurat"/>
95 <param name="n_bin" value="20"/>
96 <param name="min_mean" value="0.0125"/>
97 <param name="max_mean" value="3"/>
98 <param name="min_disp" value="0.5"/>
99 <param name="max_disp" value="1e9"/>
100 <output name="output_h5" ftype="h5">
101 <assert_contents>
102 <has_h5_keys keys="uns/hvg"/>
103 </assert_contents>
104 </output>
105 </test>
106 <test>
107 <param name="input_obj_file" value="normalise_data.h5"/>
108 <param name="never_hvg" value="never_hvg.txt"/>
66 <param name="input_format" value="anndata"/> 109 <param name="input_format" value="anndata"/>
67 <param name="output_format" value="anndata"/> 110 <param name="output_format" value="anndata"/>
68 <param name="flavor" value="seurat"/> 111 <param name="flavor" value="seurat"/>
69 <param name="n_bin" value="20"/> 112 <param name="n_bin" value="20"/>
70 <param name="min_mean" value="0.0125"/> 113 <param name="min_mean" value="0.0125"/>