Mercurial > repos > ebi-gxa > scanpy_find_variable_genes

comparison scanpy-find-variable-genes.xml @ 12:f952b39f0794 draft

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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 14:03:04 +0000
parents 1c59a010bb44
children 79da59a0b180
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11:7793c8284aa5 12:f952b39f0794
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>