Mercurial > repos > ebi-gxa > scanpy_regress_variable

comparison scanpy-regress-variable.xml @ 0:6c990f8ccad3 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 4846776f55931e176f7e77af7c185ec6fec7d142"
author ebi-gxa
date Mon, 16 Sep 2019 08:22:16 -0400
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children 203fac3b1ba3
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-1:000000000000 0:6c990f8ccad3
1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy0">
3 <description>variables that might introduce batch effect</description>
4 <macros>
5 <import>scanpy_macros2.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-regress
11 --keys '${variable_keys}'
12 @INPUT_OPTS@
13 @OUTPUT_OPTS@
14 ]]></command>
15
16 <inputs>
17 <expand macro="input_object_params"/>
18 <expand macro="output_object_params"/>
19 <param name="variable_keys" type="text" label="Variables to regress out" help="Use comma to separate multiple variables"/>
20 </inputs>
21
22 <outputs>
23 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/>
24 </outputs>
25
26 <tests>
27 <test>
28 <param name="input_obj_file" value="find_variable_genes.h5"/>
29 <param name="input_format" value="anndata"/>
30 <param name="output_format" value="anndata"/>
31 <param name="variable_keys" value="n_counts"/>
32 <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/>
33 </test>
34 </tests>
35
36 <help><![CDATA[
37 .. class:: infomark
38
39 **What it does**
40
41 Regress out unwanted source of variance (`scanpy.pp.regress_out`)
42
43 @HELP@
44
45 @VERSION_HISTORY@
46 ]]></help>
47 <expand macro="citations"/>
48 </tool>