Mercurial > repos > ebi-gxa > scanpy_filter_cells
comparison scanpy-filter-cells.xml @ 0:9f0ca1641ab2 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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date | Wed, 03 Apr 2019 11:12:31 -0400 |
parents | |
children | dcfb23758646 |
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-1:000000000000 | 0:9f0ca1641ab2 |
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1 <?xml version="1.0" encoding="utf-8"?> | |
2 <tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy0"> | |
3 <description>based on counts and numbers of genes expressed</description> | |
4 <macros> | |
5 <import>scanpy_macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 ln -s '${input_obj_file}' input.h5 && | |
10 PYTHONIOENCODING=utf-8 scanpy-filter-cells.py | |
11 -i input.h5 | |
12 -f '${input_format}' | |
13 -o output.h5 | |
14 -F '${output_format}' | |
15 #if $parameters | |
16 #set pars = ','.join([str($p['name']) for $p in $parameters]) | |
17 -p '${pars}' | |
18 #set mins = ','.join([str($p['min']) for $p in $parameters]) | |
19 -l '${mins}' | |
20 #set maxs = ','.join([str($p['max']) for $p in $parameters]) | |
21 -j '${maxs}' | |
22 #end if | |
23 #if $subset | |
24 -s '${subset}' | |
25 #end if | |
26 ]]></command> | |
27 | |
28 <inputs> | |
29 <expand macro="input_object_params"/> | |
30 <expand macro="output_object_params"/> | |
31 <repeat name="parameters" title="Parameters used to filter cells" min="1"> | |
32 <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts"> | |
33 <option value="n_genes">n_genes</option> | |
34 <option value="n_counts">n_counts</option> | |
35 </param> | |
36 <param name="min" type="float" value="0" min="0" label="Min value"/> | |
37 <param name="max" type="float" value="1e9" label="Max value"/> | |
38 </repeat> | |
39 <param name="subset" argument="--subset-list" type="data" format="tsv" optional="true" label="List of barcodes"/> | |
40 </inputs> | |
41 | |
42 <outputs> | |
43 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered cells"/> | |
44 </outputs> | |
45 | |
46 <tests> | |
47 <test> | |
48 <param name="input_obj_file" value="read_10x.h5"/> | |
49 <param name="input_format" value="anndata"/> | |
50 <param name="output_format" value="anndata"/> | |
51 <repeat name="parameters"> | |
52 <param name="name" value="n_genes"/> | |
53 <param name="min" value="200"/> | |
54 <param name="max" value="2500"/> | |
55 </repeat> | |
56 <repeat name="parameters"> | |
57 <param name="name" value="n_counts"/> | |
58 <param name="min" value="0"/> | |
59 <param name="max" value="1e9"/> | |
60 </repeat> | |
61 <output name="output_h5" file="filter_cells.h5" ftype="h5" compare="sim_size"/> | |
62 </test> | |
63 </tests> | |
64 | |
65 <help><![CDATA[ | |
66 ======================================================================================== | |
67 Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`) | |
68 ======================================================================================== | |
69 | |
70 For instance, only keep cells with at least `min_counts` counts or | |
71 `min_genes` genes expressed. This is to filter measurement outliers, i.e., | |
72 "unreliable" observations. | |
73 | |
74 @HELP@ | |
75 | |
76 @VERSION_HISTORY@ | |
77 ]]></help> | |
78 <expand macro="citations"/> | |
79 </tool> |