Mercurial > repos > ebi-gxa > scanpy_regress_variable
comparison scanpy-regress-variable.xml @ 19:59d3ce1cfaa8 draft
"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 |
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date | Wed, 05 May 2021 12:13:12 +0000 |
parents | 8205e95227e4 |
children | 1200b55768ce |
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18:1ad1d9713563 | 19:59d3ce1cfaa8 |
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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> |