Mercurial > repos > ebi-gxa > scanpy_filter_genes
comparison scanpy-filter-genes.xml @ 0:d1b97a5d5a8d 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 11:10:01 -0400 |
parents | |
children | 7aebd6265a97 |
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-1:000000000000 | 0:d1b97a5d5a8d |
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1 <?xml version="1.0" encoding="utf-8"?> | |
2 <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy1"> | |
3 <description>based on counts and numbers of cells 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 '${input_obj_file}' input.h5 && | |
10 PYTHONIOENCODING=utf-8 scanpy-filter-genes.py | |
11 -i input.h5 | |
12 -f '${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 @EXPORT_MTX_OPTS@ | |
27 ]]></command> | |
28 | |
29 <inputs> | |
30 <expand macro="input_object_params"/> | |
31 <expand macro="output_object_params"/> | |
32 <repeat name="parameters" title="Parameters used to filter genes" min="1"> | |
33 <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_cells or n_counts"> | |
34 <option value="n_cells">n_cells</option> | |
35 <option value="n_counts">n_counts</option> | |
36 </param> | |
37 <param name="min" type="float" value="0" min="0" label="Min value"/> | |
38 <param name="max" type="float" value="1e9" label="Max value"/> | |
39 </repeat> | |
40 <param name="subset" argument="--subset-list" type="data" format="tsv" optional="true" label="List of gene IDs or symbols"/> | |
41 <expand macro="export_mtx_params"/> | |
42 </inputs> | |
43 | |
44 <outputs> | |
45 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered genes"/> | |
46 <expand macro="export_mtx_outputs"/> | |
47 </outputs> | |
48 | |
49 <tests> | |
50 <test> | |
51 <param name="input_obj_file" value="filter_cells.h5"/> | |
52 <param name="input_format" value="anndata"/> | |
53 <param name="output_format" value="anndata"/> | |
54 <repeat name="parameters"> | |
55 <param name="name" value="n_cells"/> | |
56 <param name="min" value="3"/> | |
57 <param name="max" value="1e9"/> | |
58 </repeat> | |
59 <repeat name="parameters"> | |
60 <param name="name" value="n_counts"/> | |
61 <param name="min" value="0"/> | |
62 <param name="max" value="1e9"/> | |
63 </repeat> | |
64 <output name="output_h5" file="filter_genes.h5" ftype="h5" compare="sim_size"/> | |
65 </test> | |
66 </tests> | |
67 | |
68 <help><![CDATA[ | |
69 =================================================================== | |
70 Filter genes based on number of cells or counts (`pp.filter_genes`) | |
71 =================================================================== | |
72 | |
73 Keep genes that have at least `min_counts` counts or are expressed in at | |
74 least `min_cells` cells or have at most `max_counts` counts or are expressed | |
75 in at most `max_cells` cells. | |
76 | |
77 Only provide one of the optional parameters `min_counts`, `min_cells`, | |
78 `max_counts`, `max_cells` per call. | |
79 | |
80 | |
81 @HELP@ | |
82 | |
83 @VERSION_HISTORY@ | |
84 ]]></help> | |
85 <expand macro="citations"/> | |
86 </tool> |