Mercurial > repos > ebi-gxa > scanpy_regress_variable

comparison scanpy-regress-variable.xml @ 1:203fac3b1ba3 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 1cc5d2101b8b14fa99e11b01714e5544704e669f
author ebi-gxa
date Tue, 15 Oct 2019 05:21:49 -0400
parents 6c990f8ccad3
children b174cb4cb89e
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0:6c990f8ccad3 1:203fac3b1ba3
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy0"> 2 <tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy1">
3 <description>variables that might introduce batch effect</description> 3 <description>variables that might introduce batch effect</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"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 && 9 #if $variable_keys
10 PYTHONIOENCODING=utf-8 scanpy-regress 10 ln -s '${input_obj_file}' input.h5 &&
11 --keys '${variable_keys}' 11 PYTHONIOENCODING=utf-8 scanpy-regress
12 @INPUT_OPTS@ 12 --keys '${variable_keys}'
13 @OUTPUT_OPTS@ 13 @INPUT_OPTS@
14 @OUTPUT_OPTS@
15 #else
16 echo "No regression variables passed, simply passing original input as output unchanged.";
17 cp '${input_obj_file}' '${output_h5}'
18 #end if
14 ]]></command> 19 ]]></command>
15 20
16 <inputs> 21 <inputs>
17 <expand macro="input_object_params"/> 22 <expand macro="input_object_params"/>
18 <expand macro="output_object_params"/> 23 <expand macro="output_object_params"/>
19 <param name="variable_keys" type="text" label="Variables to regress out" help="Use comma to separate multiple variables"/> 24 <param name="variable_keys" type="text" label="Variables to regress out" help="Use comma to separate multiple variables. Not supplying variables will simply pass the input data as output unchanged.">
25 <sanitizer>
26 <valid initial="string.printable"/>
27 </sanitizer>
28 </param>
20 </inputs> 29 </inputs>
21 30
22 <outputs> 31 <outputs>
23 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/> 32 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/>
24 </outputs> 33 </outputs>