Mercurial > repos > ebi-gxa > scanpy_scale_data
comparison scanpy-scale-data.xml @ 0:96b851e96dd0 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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date | Wed, 03 Apr 2019 11:09:38 -0400 |
parents | |
children | 9acb5f068e6b |
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1 <?xml version="1.0" encoding="utf-8"?> | |
2 <tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy1"> | |
3 <description>to make expression variance the same for all genes</description> | |
4 <macros> | |
5 <import>scanpy_macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 ln -s '${input_obj_file}' input.h5 && | |
10 PYTHONIOENCODING=utf-8 scanpy-scale-data.py | |
11 -i input.h5 | |
12 -f '${input_format}' | |
13 -o output.h5 | |
14 -F '${output_format}' | |
15 #if $scale_max | |
16 -x '${scale_max}' | |
17 #end if | |
18 #if $var_to_regress | |
19 -V '${var_to_regress}' | |
20 #end if | |
21 #if $do_log | |
22 --do-log | |
23 #end if | |
24 #if $zero_center | |
25 --zero-center | |
26 #end if | |
27 ]]></command> | |
28 | |
29 <inputs> | |
30 <expand macro="input_object_params"/> | |
31 <expand macro="output_object_params"/> | |
32 <param name="do_log" argument="--do-log" type="boolean" checked="true" label="Do log(x+1) transformation"/> | |
33 <param name="zero_center" argument="--zero-center" type="boolean" checked="true" label="Zero center data before scaling"/> | |
34 <param name="var_to_regress" argument="--var-to-regress" type="text" optional="true" label="Variable(s) to regress out"> | |
35 <option value="n_counts">n_counts</option> | |
36 </param> | |
37 <param name="scale_max" argument="--scale-max" type="float" optional="true" label="Truncate to this value after scaling"/> | |
38 </inputs> | |
39 | |
40 <outputs> | |
41 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/> | |
42 </outputs> | |
43 | |
44 <tests> | |
45 <test> | |
46 <param name="input_obj_file" value="find_variable_genes.h5"/> | |
47 <param name="input_format" value="anndata"/> | |
48 <param name="output_format" value="anndata"/> | |
49 <param name="do_log" value="true"/> | |
50 <param name="zero_center" value="true"/> | |
51 <param name="scale_max" value="10"/> | |
52 <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/> | |
53 </test> | |
54 </tests> | |
55 | |
56 <help><![CDATA[ | |
57 .. class:: infomark | |
58 | |
59 **What it does** | |
60 | |
61 Scale data to unit variance and zero mean (`pp.scale`) | |
62 Regress out unwanted sources of variation (`pp.regress_out`) | |
63 | |
64 Regress out unwanted sources of variation, using simple linear regression. This is | |
65 inspired by Seurat's `regressOut` function in R. | |
66 | |
67 @HELP@ | |
68 | |
69 @VERSION_HISTORY@ | |
70 ]]></help> | |
71 <expand macro="citations"/> | |
72 </tool> |