Mercurial > repos > ebi-gxa > scanpy_filter_genes

comparison scanpy-filter-genes.xml @ 3:77fbe74247c2 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 ccd9b839849600b1aa3b6cf54f667575a5f2da9d
author ebi-gxa
date Fri, 25 Oct 2019 08:21:35 -0400
parents a797a810d7e9
children fa6c08064fc1
comparison
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2:a797a810d7e9 3:77fbe74247c2
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-filter-genes 10 PYTHONIOENCODING=utf-8 scanpy-filter-genes
11 #if $parameters 11 #if $parameters
12 #set pars = ' '.join(['--param {name} {min} {max}'.format(**$p) for $p in $parameters]) 12 #set pars = ' '.join(['--param g:{name} {min} {max}'.format(**$p) for $p in $parameters])
13 ${pars} 13 ${pars}
14 #end if 14 #end if
15 #if $categories 15 #if $categories
16 #set cats = ' '.join(['--category {name} {values}'.format(**$c) for $c in $categories]) 16 #set cats = ' '.join(['--category g:{name} {values}'.format(**$c) for $c in $categories])
17 ${cats} 17 ${cats}
18 #end if 18 #end if
19 #if $subsets 19 #if $subsets
20 #set subs = ' '.join(['--subsets {name} {subset}'.format(**$s) for $s in $subsets]) 20 #set subs = ' '.join(['--subset g:{name} {subset}'.format(**$s) for $s in $subsets])
21 ${subs} 21 ${subs}
22 #end if 22 #end if
23 @INPUT_OPTS@ 23 @INPUT_OPTS@
24 @OUTPUT_OPTS@ 24 @OUTPUT_OPTS@
25 ]]></command> 25 ]]></command>
26 26
27 <inputs> 27 <inputs>
28 <expand macro="input_object_params"/> 28 <expand macro="input_object_params"/>
29 <expand macro="output_object_params"/> 29 <expand macro="output_object_params"/>
30 30
31 <repeat name="parameters" title="Parameters used to filter cells" min="1"> 31 <repeat name="parameters" title="Parameters used to filter genes" min="1">
32 <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_genes or n_counts"> 32 <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_genes or n_counts">
33 <option value="n_cells">n_cells</option> 33 <option value="n_cells">n_cells</option>
34 <option value="gene:n_counts">n_counts</option> 34 <option value="n_counts">n_counts</option>
35 </param> 35 </param>
36 <param name="min" type="float" min="0" value="0" label="Min value"/> 36 <param name="min" type="float" min="0" value="0" label="Min value"/>
37 <param name="max" type="float" min="0" value="1e9" label="Max value"/> 37 <param name="max" type="float" min="0" value="1e9" label="Max value"/>
38 </repeat> 38 </repeat>
39 39
40 <repeat name="categories" title="Categories used to filter genes" min="0"> 40 <repeat name="categories" title="Categories used to filter genes" min="0">
41 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> 41 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
42 <param name="values" type="text" value="" label="Comma-separated values"/> 42 <param name="values" type="text" value="" label="Comma-separated values to keep"/>
43 </repeat> 43 </repeat>
44 44
45 <repeat name="subsets" title="Subsets used to filter genes" min="0"> 45 <repeat name="subsets" title="Subsets used to filter genes" min="0">
46 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> 46 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
47 <param name="subset" type="data" format="tabular" label="List of values"/> 47 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>
48 </repeat> 48 </repeat>
49 <expand macro="export_mtx_params"/> 49 <expand macro="export_mtx_params"/>
50 </inputs> 50 </inputs>
51 51
52 <outputs> 52 <outputs>
63 <param name="name" value="n_cells"/> 63 <param name="name" value="n_cells"/>
64 <param name="min" value="3"/> 64 <param name="min" value="3"/>
65 <param name="max" value="1e9"/> 65 <param name="max" value="1e9"/>
66 </repeat> 66 </repeat>
67 <repeat name="parameters"> 67 <repeat name="parameters">
68 <param name="name" value="gene:n_counts"/> 68 <param name="name" value="n_counts"/>
69 <param name="min" value="0"/> 69 <param name="min" value="0"/>
70 <param name="max" value="1e9"/> 70 <param name="max" value="1e9"/>
71 </repeat> 71 </repeat>
72 <output name="output_h5" file="filter_genes.h5" ftype="h5" compare="sim_size"/> 72 <output name="output_h5" file="filter_genes.h5" ftype="h5" compare="sim_size"/>
73 </test> 73 </test>
74 </tests> 74 </tests>
75 75
76 <help><![CDATA[ 76 <help><![CDATA[
77 =================================================================== 77 =====================================================================
78 Filter genes based on number of cells or counts (`pp.filter_genes`) 78 Filter genes based on arbitrary attributes (`scanpy.pp.filter_genes`)
79 =================================================================== 79 =====================================================================
80 80
81 Keep genes that have at least `min_counts` counts or are expressed in at 81 Keep genes that have at least `min_counts` counts or are expressed in at
82 least `min_cells` cells or have at most `max_counts` counts or are expressed 82 least `min_cells` cells or have at most `max_counts` counts or are expressed
83 in at most `max_cells` cells. 83 in at most `max_cells` cells. Other gene attributes can be used for filtering
84 84 too if available.
85 Only provide one of the optional parameters `min_counts`, `min_cells`,
86 `max_counts`, `max_cells` per call.
87 85
88 86
89 @HELP@ 87 @HELP@
90 88
91 @VERSION_HISTORY@ 89 @VERSION_HISTORY@