Mercurial > repos > ebi-gxa > scanpy_filter_cells
comparison scanpy-filter-cells.xml @ 8:8d97bee137b5 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 367d978e52fac9467a804009c5013f53c06765f0
author | ebi-gxa |
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date | Tue, 26 Nov 2019 05:55:39 -0500 |
parents | 9c65f1de489b |
children | c1362eee9eee |
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7:9c65f1de489b | 8:8d97bee137b5 |
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1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
2 <tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy6"> | 2 <tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy7"> |
3 <description>based on counts and numbers of genes expressed</description> | 3 <description>based on counts and numbers of genes expressed</description> |
4 <macros> | 4 <macros> |
5 <import>scanpy_macros2.xml</import> | 5 <import>scanpy_macros2.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
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 $parameters |
15 #set pars = ' '.join(["--param 'c:{name}' {min} {max}".format(**$p) for $p in $parameters]) | 15 #for $p in $parameters |
16 ${pars} | 16 #set $min = $p.min |
17 #set $max = $p.max | |
18 #if $p.name.startswith('pct_') | |
19 #set $min = float($min) / 100 | |
20 #set $max = float($max) / 100 | |
21 #end if | |
22 --param 'c:$p.name' $min $max | |
23 #end for | |
17 #end if | 24 #end if |
18 #if $categories | 25 #if $categories |
19 #set cats = ' '.join(["--category 'c:{name}' '{negate}{values}'".format(**$c) for $c in $categories]) | 26 #set cats = ' '.join(["--category 'c:{name}' '{negate}{values}'".format(**$c) for $c in $categories]) |
20 ${cats} | 27 ${cats} |
21 #end if | 28 #end if |
33 <expand macro="output_object_params"/> | 40 <expand macro="output_object_params"/> |
34 | 41 |
35 <param name="gene_name" type="text" optional="true" label="Name of the column in `anndata.var` that contains gene name" | 42 <param name="gene_name" type="text" optional="true" label="Name of the column in `anndata.var` that contains gene name" |
36 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"/> | 43 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"/> |
37 | 44 |
38 <repeat name="parameters" title="Parameters used to filter cells" min="1"> | 45 <repeat name="parameters" title="Parameters to select cells to keep" min="1"> |
39 <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts"> | 46 <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts"> |
40 <option value="n_genes">n_genes</option> | 47 <option value="n_genes">n_genes</option> |
41 <option value="n_counts">n_counts</option> | 48 <option value="n_counts">n_counts</option> |
42 <option value="pct_counts_mito">pct_counts_mito (only usable if MT genes are flagged)</option> | 49 <option value="pct_counts_mito">pct_counts_mito (only usable if MT genes are flagged or has been pre-calculated)</option> |
43 </param> | 50 </param> |
44 <param name="min" type="float" value="0" min="0" label="Min value"/> | 51 <param name="min" type="float" value="0" min="0" label="Min value" help="Cells with value below min will be discarded."/> |
45 <param name="max" type="float" value="1e9" label="Max value"/> | 52 <param name="max" type="float" value="1e9" label="Max value" help="Cells with value above max will be discarded."/> |
46 </repeat> | 53 </repeat> |
47 | 54 |
48 <repeat name="categories" title="Categories used to filter cells" min="0"> | 55 <repeat name="categories" title="Categories to select cells to keep (unless negate is checked)" min="0"> |
49 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> | 56 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> |
50 <param name="values" type="text" value="" label="Comma-separated list of categories"/> | 57 <param name="values" type="text" value="" label="Comma-separated list of categories" help="Cells with these values in this categorical variable will be kept."/> |
51 <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."/> | 58 <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."/> |
52 </repeat> | 59 </repeat> |
53 | 60 |
54 <repeat name="subsets" title="Subsets used to filter cells" min="0"> | 61 <repeat name="subsets" title="Subsets to select cells to keep" min="0"> |
55 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> | 62 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> |
56 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/> | 63 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/> |
57 </repeat> | 64 </repeat> |
65 <param name="force_recalc" label="Force recalculation of QC vars" type="boolean" truevalue="--force-recalc" falsevalue="" help="If set, it will recalculate pcts and other existing QC vars, overwriting existing ones."/> | |
58 <expand macro="export_mtx_params"/> | 66 <expand macro="export_mtx_params"/> |
59 </inputs> | 67 </inputs> |
60 | 68 |
61 <outputs> | 69 <outputs> |
62 <expand macro="output_data_obj" description="Filtered cells"/> | 70 <expand macro="output_data_obj" description="Filtered cells"/> |