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comparison scanpy-filter-cells.xml @ 2:c23d0ff783d4 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 08:25:27 -0400
parents dcfb23758646
children 8e48fa9618c1
comparison
equal deleted inserted replaced
1:dcfb23758646 2:c23d0ff783d4
10 PYTHONIOENCODING=utf-8 scanpy-filter-cells 10 PYTHONIOENCODING=utf-8 scanpy-filter-cells
11 #if $gene_name 11 #if $gene_name
12 --gene-name '${gene_name}' 12 --gene-name '${gene_name}'
13 #end if 13 #end if
14 #if $parameters 14 #if $parameters
15 #set pars = ' '.join(['--param {name} {min} {max}'.format(**$p) for $p in $parameters]) 15 #set pars = ' '.join(['--param c:{name} {min} {max}'.format(**$p) for $p in $parameters])
16 ${pars} 16 ${pars}
17 #end if 17 #end if
18 #if $categories 18 #if $categories
19 #set cats = ' '.join(['--category {name} {values}'.format(**$c) for $c in $categories]) 19 #set cats = ' '.join(['--category c:{name} {values}'.format(**$c) for $c in $categories])
20 ${cats} 20 ${cats}
21 #end if 21 #end if
22 #if $subsets 22 #if $subsets
23 #set subs = ' '.join(['--subsets {name} {subset}'.format(**$s) for $c in $subsets]) 23 #set subs = ' '.join(['--subset c:{name} {subset}'.format(**$s) for $s in $subsets])
24 ${subs} 24 ${subs}
25 #end if 25 #end if
26 @INPUT_OPTS@ 26 @INPUT_OPTS@
27 @OUTPUT_OPTS@ 27 @OUTPUT_OPTS@
28 ]]></command> 28 ]]></command>
29 29
30 <inputs> 30 <inputs>
31 <expand macro="input_object_params"/> 31 <expand macro="input_object_params"/>
32 <expand macro="output_object_params"/> 32 <expand macro="output_object_params"/>
33 33
34 <param name="gene_name" type="text" value="index" label="Name of the column in `anndata.var` that contains gene name" 34 <param name="gene_name" type="text" optional="true" label="Name of the column in `anndata.var` that contains gene name"
35 help="This is used for flagging mitochondria genes (starting with 'MT-')"/> 35 help="Used for flagging mitochondria genes (starting with 'MT-'). Leave empty if gene table already has a boolean column called 'mito' that flags MT genes"/>
36 36
37 <repeat name="parameters" title="Parameters used to filter cells" min="1"> 37 <repeat name="parameters" title="Parameters used to filter cells" min="1">
38 <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts"> 38 <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts">
39 <option value="n_genes">n_genes</option> 39 <option value="n_genes">n_genes</option>
40 <option value="cell:n_counts">n_counts</option> 40 <option value="n_counts">n_counts</option>
41 <option value="pct_counts_mito">pct_counts_mito</option> 41 <option value="pct_counts_mito">pct_counts_mito (only usable if MT genes are flagged)</option>
42 </param> 42 </param>
43 <param name="min" type="float" value="0" min="0" label="Min value"/> 43 <param name="min" type="float" value="0" min="0" label="Min value"/>
44 <param name="max" type="float" value="1e9" label="Max value"/> 44 <param name="max" type="float" value="1e9" label="Max value"/>
45 </repeat> 45 </repeat>
46 46
47 <repeat name="categories" title="Categories used to filter cells" min="0"> 47 <repeat name="categories" title="Categories used to filter cells" min="0">
48 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> 48 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
49 <param name="values" type="text" value="" label="Comma-separated values"/> 49 <param name="values" type="text" value="" label="Comma-separated values to keep"/>
50 </repeat> 50 </repeat>
51 51
52 <repeat name="subsets" title="Subsets used to filter cells" min="0"> 52 <repeat name="subsets" title="Subsets used to filter cells" min="0">
53 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> 53 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
54 <param name="subset" type="data" format="tabular" label="List of values"/> 54 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>
55 </repeat> 55 </repeat>
56 <expand macro="export_mtx_params"/> 56 <expand macro="export_mtx_params"/>
57 </inputs> 57 </inputs>
58 58
59 <outputs> 59 <outputs>
70 <param name="name" value="n_genes"/> 70 <param name="name" value="n_genes"/>
71 <param name="min" value="200"/> 71 <param name="min" value="200"/>
72 <param name="max" value="2500"/> 72 <param name="max" value="2500"/>
73 </repeat> 73 </repeat>
74 <repeat name="parameters"> 74 <repeat name="parameters">
75 <param name="name" value="cell:n_counts"/> 75 <param name="name" value="n_counts"/>
76 <param name="min" value="0"/> 76 <param name="min" value="0"/>
77 <param name="max" value="1e9"/> 77 <param name="max" value="1e9"/>
78 </repeat> 78 </repeat>
79 <output name="output_h5" file="output.h5" ftype="h5" compare="sim_size"/> 79 <output name="output_h5" file="output.h5" ftype="h5" compare="sim_size"/>
80 </test> 80 </test>