Mercurial > repos > ebi-gxa > scanpy_regress_variable

comparison scanpy-regress-variable.xml @ 19:59d3ce1cfaa8 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 ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
author ebi-gxa
date Wed, 05 May 2021 12:13:12 +0000
parents 8205e95227e4
children 1200b55768ce
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18:1ad1d9713563 19:59d3ce1cfaa8
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #if $variable_keys 9 #if $variable_keys
10 ln -s '${input_obj_file}' input.h5 && 10 ln -s '${input_obj_file}' input.h5 &&
11 PYTHONIOENCODING=utf-8 scanpy-regress 11 PYTHONIOENCODING=utf-8 scanpy-regress
12 --keys '${variable_keys}' 12 --keys '${variable_keys}'
13 @SAVE_MATRIX_OPTS@
13 @INPUT_OPTS@ 14 @INPUT_OPTS@
14 @OUTPUT_OPTS@ 15 @OUTPUT_OPTS@
15 #else 16 #else
16 echo "No regression variables passed, simply passing original input as output unchanged." && cp '${input_obj_file}' output.h5 17 echo "No regression variables passed, simply passing original input as output unchanged." && cp '${input_obj_file}' output.h5
17 #end if 18 #end if
23 <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."> 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.">
24 <sanitizer> 25 <sanitizer>
25 <valid initial="string.printable"/> 26 <valid initial="string.printable"/>
26 </sanitizer> 27 </sanitizer>
27 </param> 28 </param>
29 <expand macro="save_matrix_params"/>
28 </inputs> 30 </inputs>
29 31
30 <outputs> 32 <outputs>
31 <expand macro="output_data_obj" description="Regressed out ${variable_keys}"/> 33 <expand macro="output_data_obj" description="Regressed out ${variable_keys}"/>
32 </outputs> 34 </outputs>