Mercurial > repos > ebi-gxa > scanpy_find_variable_genes
comparison scanpy-find-variable-genes.xml @ 12:f952b39f0794 draft
"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 |
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date | Mon, 07 Sep 2020 14:03:04 +0000 |
parents | 1c59a010bb44 |
children | 79da59a0b180 |
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11:7793c8284aa5 | 12:f952b39f0794 |
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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@+galaxy10" profile="@PROFILE@"> | 2 <tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy0" 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"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 ln -s '${input_obj_file}' input.h5 && | 9 ln -s '${input_obj_file}' input.h5 && |
10 PYTHONIOENCODING=utf-8 scanpy-find-variable-genes | 10 PYTHONIOENCODING=utf-8 scanpy-find-variable-genes |
11 --flavor '${method.flavor}' | 11 --flavor '${flavor}' |
12 #if $method.flavor == 'seurat' | 12 #if $min_mean |
13 --mean-limits ${method.min_mean} ${method.max_mean} | 13 --mean-limits ${min_mean} ${max_mean} |
14 --disp-limits ${method.min_disp} ${method.max_disp} | 14 #end if |
15 #else | 15 #if $min_disp |
16 --n-top-genes ${method.n_top_gene} | 16 --disp-limits ${min_disp} ${max_disp} |
17 #end if | |
18 #if $n_top_gene | |
19 --n-top-genes ${n_top_gene} | |
20 #end if | |
21 #if $span | |
22 --span ${span} | |
17 #end if | 23 #end if |
18 --n-bins '${n_bin}' | 24 --n-bins '${n_bin}' |
19 ${filter} | 25 ${filter} |
20 @INPUT_OPTS@ | 26 @INPUT_OPTS@ |
21 @OUTPUT_OPTS@ | 27 @OUTPUT_OPTS@ |
22 ]]></command> | 28 ]]></command> |
23 | 29 |
24 <inputs> | 30 <inputs> |
25 <expand macro="input_object_params"/> | 31 <expand macro="input_object_params"/> |
26 <expand macro="output_object_params"/> | 32 <expand macro="output_object_params"/> |
27 <conditional name="method"> | 33 <param name="flavor" argument="--flavor" type="select" label="Flavor of computing normalised dispersion"> |
28 <param name="flavor" argument="--flavor" type="select" label="Flavor of computing normalised dispersion"> | 34 <option value="seurat" selected="true">Seurat</option> |
29 <option value="seurat" selected="true">Seurat</option> | 35 <option value="cell_ranger">Cell-ranger</option> |
30 <option value="cell_ranger">Cell-ranger</option> | 36 <option value="seurat_v3" selected="true">Seurat V3</option> |
31 </param> | 37 </param> |
32 <when value="seurat"> | 38 <param name="min_mean" argument="--min-mean" type="float" min="0" value="0.0125" optional="true" |
33 <param name="min_mean" argument="--min-mean" type="float" min="0" value="0.0125" | 39 label="Min value for normalised mean expression (in log1p scale), ignored if flavor='seurat_v3'"/> |
34 label="Min value for normalised mean expression (in log1p scale)"/> | 40 <param name="max_mean" argument="--max-mean" type="float" min="0" value="3" optional="true" |
35 <param name="max_mean" argument="--max-mean" type="float" min="0" value="3" | 41 label="Max value for normalised mean expresssion (in log1p scale), Ignored if flavor='seurat_v3'"/> |
36 label="Max value for normalised mean expresssion (in log1p scale)"/> | 42 <param name="min_disp" argument="--min-disp" type="float" min="0" value="0.5" optional="true" |
37 <param name="min_disp" argument="--min-disp" type="float" min="0" value="0.5" | 43 label="Min value for dispersion of expression, ignored if flavor='seurat_v3'"/> |
38 label="Min value for dispersion of expression"/> | 44 <param name="max_disp" argument="--max-disp" type="float" min="0" value="50" optional="true" |
39 <param name="max_disp" argument="--max-disp" type="float" min="0" value="50" | 45 label="Max value for dispersion of expresssion, ignored if flavor='seurat_v3'"/> |
40 label="Max value for dispersion of expresssion"/> | 46 <param name="n_top_gene" argument="--n-top-genes" type="integer" value="2000" optional="true" |
41 </when> | 47 label="Number of top variable genes to keep, mandatory if flavor='seurat_v3'"/> |
42 <when value="cell_ranger"> | 48 <param name="span" argument="--span" type="float" min="0" max="1" value="0.3" optional="true" |
43 <param name="n_top_gene" argument="--n-top-genes" type="integer" value="2000" | 49 label="The fraction of the data (cells) used when estimating the variance in the loess model fit if flavor='seurat_v3'"/> |
44 label="Number of top variable genes to keep"/> | |
45 </when> | |
46 </conditional> | |
47 <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/> | 50 <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/> |
48 <param name="filter" argument="--subset" type="boolean" truevalue="--subset" falsevalue="" checked="false" | 51 <param name="filter" argument="--subset" type="boolean" truevalue="--subset" falsevalue="" checked="false" |
49 label="Remove genes not marked as highly variable"/> | 52 label="Remove genes not marked as highly variable" help="When set, inplace subset to highly-variable genes, otherwise only flag highly-variable genes."/> |
53 <param name="batch_key" argument="--batch-key" type="text" label="Batch key" 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."/> | |
50 </inputs> | 54 </inputs> |
51 | 55 |
52 <outputs> | 56 <outputs> |
53 <expand macro="output_data_obj" description="Variable genes"/> | 57 <expand macro="output_data_obj" description="Variable genes"/> |
54 </outputs> | 58 </outputs> |