Mercurial > repos > ebi-gxa > scanpy_run_umap
comparison scanpy-filter-genes.xml.bak @ 8:41f6078040da draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit cbe12e02ee9ff5692be7547bdbe28fd1cd013a92
author | ebi-gxa |
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date | Thu, 20 Feb 2020 10:18:38 -0500 |
parents | 3bd1152dd854 |
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7:aa85725f43a2 | 8:41f6078040da |
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1 <?xml version="1.0" encoding="utf-8"?> | |
2 <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy3"> | |
3 <description>based on counts and numbers of cells expressed</description> | |
4 <macros> | |
5 <import>scanpy_macros2.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 | |
11 #if $parameters | |
12 #set pars = ' '.join(['--param g:{name} {min} {max}'.format(**$p) for $p in $parameters]) | |
13 ${pars} | |
14 #end if | |
15 #if $categories | |
16 #set cats = ' '.join(['--category g:{name} {negate}{values}'.format(**$c) for $c in $categories]) | |
17 ${cats} | |
18 #end if | |
19 #if $subsets | |
20 #set subs = ' '.join(['--subset g:{name} {subset}'.format(**$s) for $s in $subsets]) | |
21 ${subs} | |
22 #end if | |
23 @INPUT_OPTS@ | |
24 @OUTPUT_OPTS@ | |
25 @EXPORT_MTX_OPTS@ | |
26 ]]></command> | |
27 | |
28 <inputs> | |
29 <expand macro="input_object_params"/> | |
30 <expand macro="output_object_params"/> | |
31 | |
32 <repeat name="parameters" title="Parameters used to filter genes" min="1"> | |
33 <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_genes or n_counts"> | |
34 <option value="n_cells">n_cells</option> | |
35 <option value="n_counts">n_counts</option> | |
36 </param> | |
37 <param name="min" type="float" min="0" value="0" label="Min value"/> | |
38 <param name="max" type="float" min="0" value="1e9" label="Max value"/> | |
39 </repeat> | |
40 | |
41 <repeat name="categories" title="Categories used to filter genes" min="0"> | |
42 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> | |
43 <param name="values" type="text" value="" label="Comma-separated list of categories"/> | |
44 <param name="negate" type="boolean" truevalue="!" falsevalue="" checked="false" label="Apply as negative filter" help="If enabled, specified categories will be removed rather than retained."/> | |
45 </repeat> | |
46 | |
47 <repeat name="subsets" title="Subsets used to filter genes" min="0"> | |
48 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> | |
49 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/> | |
50 </repeat> | |
51 <expand macro="export_mtx_params"/> | |
52 </inputs> | |
53 | |
54 <outputs> | |
55 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered genes"/> | |
56 <expand macro="export_mtx_outputs"/> | |
57 </outputs> | |
58 | |
59 <tests> | |
60 <test> | |
61 <param name="input_obj_file" value="filter_cells.h5"/> | |
62 <param name="input_format" value="anndata"/> | |
63 <param name="output_format" value="anndata"/> | |
64 <repeat name="parameters"> | |
65 <param name="name" value="n_cells"/> | |
66 <param name="min" value="3"/> | |
67 <param name="max" value="1e9"/> | |
68 </repeat> | |
69 <repeat name="parameters"> | |
70 <param name="name" value="n_counts"/> | |
71 <param name="min" value="0"/> | |
72 <param name="max" value="1e9"/> | |
73 </repeat> | |
74 <output name="output_h5" file="filter_genes.h5" ftype="h5" compare="sim_size"/> | |
75 </test> | |
76 </tests> | |
77 | |
78 <help><![CDATA[ | |
79 ===================================================================== | |
80 Filter genes based on arbitrary attributes (`scanpy.pp.filter_genes`) | |
81 ===================================================================== | |
82 | |
83 Keep genes that have at least `min_counts` counts or are expressed in at | |
84 least `min_cells` cells or have at most `max_counts` counts or are expressed | |
85 in at most `max_cells` cells. Other gene attributes can be used for filtering | |
86 too if available. | |
87 | |
88 | |
89 @HELP@ | |
90 | |
91 @VERSION_HISTORY@ | |
92 ]]></help> | |
93 <expand macro="citations"/> | |
94 </tool> |