Mercurial > repos > ebi-gxa > scanpy_filter_genes
comparison scanpy-filter-genes.xml @ 1:7aebd6265a97 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
author | ebi-gxa |
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date | Mon, 16 Sep 2019 08:15:32 -0400 |
parents | d1b97a5d5a8d |
children | a797a810d7e9 |
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0:d1b97a5d5a8d | 1:7aebd6265a97 |
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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_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy1"> | 2 <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy1"> |
3 <description>based on counts and numbers of cells expressed</description> | 3 <description>based on counts and numbers of cells expressed</description> |
4 <macros> | 4 <macros> |
5 <import>scanpy_macros.xml</import> | 5 <import>scanpy_macros2.xml</import> |
6 </macros> | 6 </macros> |
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.py | 10 PYTHONIOENCODING=utf-8 scanpy-filter-genes |
11 -i input.h5 | 11 #if $parameters |
12 -f '${input_format}' | 12 #set pars = ' '.join(['--param {name} {min} {max}'.format(**$p) for $p in $parameters]) |
13 -o output.h5 | 13 ${pars} |
14 -F '${output_format}' | 14 #end if |
15 #if $parameters | 15 #if $categories |
16 #set pars = ','.join([str($p['name']) for $p in $parameters]) | 16 #set cats = ' '.join(['--category {name} {values}'.format(**$c) for $c in $categories]) |
17 -p '${pars}' | 17 ${cats} |
18 #set mins = ','.join([str($p['min']) for $p in $parameters]) | 18 #end if |
19 -l '${mins}' | 19 #if $subsets |
20 #set maxs = ','.join([str($p['max']) for $p in $parameters]) | 20 #set subs = ' '.join(['--subsets {name} {subset}'.format(**$s) for $c in $subsets]) |
21 -j '${maxs}' | 21 ${subs} |
22 #end if | 22 #end if |
23 #if $subset | 23 @INPUT_OPTS@ |
24 -s '${subset}' | 24 @OUTPUT_OPTS@ |
25 #end if | |
26 @EXPORT_MTX_OPTS@ | |
27 ]]></command> | 25 ]]></command> |
28 | 26 |
29 <inputs> | 27 <inputs> |
30 <expand macro="input_object_params"/> | 28 <expand macro="input_object_params"/> |
31 <expand macro="output_object_params"/> | 29 <expand macro="output_object_params"/> |
32 <repeat name="parameters" title="Parameters used to filter genes" min="1"> | 30 |
33 <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_cells or n_counts"> | 31 <repeat name="parameters" title="Parameters used to filter cells" 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"> | |
34 <option value="n_cells">n_cells</option> | 33 <option value="n_cells">n_cells</option> |
35 <option value="n_counts">n_counts</option> | 34 <option value="gene:n_counts">n_counts</option> |
36 </param> | 35 </param> |
37 <param name="min" type="float" value="0" min="0" label="Min value"/> | 36 <param name="min" type="float" min="0" value="0" label="Min value"/> |
38 <param name="max" type="float" value="1e9" label="Max value"/> | 37 <param name="max" type="float" min="0" value="1e9" label="Max value"/> |
39 </repeat> | 38 </repeat> |
40 <param name="subset" argument="--subset-list" type="data" format="tsv" optional="true" label="List of gene IDs or symbols"/> | 39 |
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"/> | |
42 <param name="values" type="text" value="" label="Comma-separated values"/> | |
43 </repeat> | |
44 | |
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"/> | |
47 <param name="subset" type="data" format="tabular" label="List of values"/> | |
48 </repeat> | |
41 <expand macro="export_mtx_params"/> | 49 <expand macro="export_mtx_params"/> |
42 </inputs> | 50 </inputs> |
43 | 51 |
44 <outputs> | 52 <outputs> |
45 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered genes"/> | 53 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered genes"/> |
55 <param name="name" value="n_cells"/> | 63 <param name="name" value="n_cells"/> |
56 <param name="min" value="3"/> | 64 <param name="min" value="3"/> |
57 <param name="max" value="1e9"/> | 65 <param name="max" value="1e9"/> |
58 </repeat> | 66 </repeat> |
59 <repeat name="parameters"> | 67 <repeat name="parameters"> |
60 <param name="name" value="n_counts"/> | 68 <param name="name" value="gene:n_counts"/> |
61 <param name="min" value="0"/> | 69 <param name="min" value="0"/> |
62 <param name="max" value="1e9"/> | 70 <param name="max" value="1e9"/> |
63 </repeat> | 71 </repeat> |
64 <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"/> |
65 </test> | 73 </test> |