Mercurial > repos > ebi-gxa > scanpy_normalise_data

comparison scanpy-normalise-data.xml @ 2:059f8d2e8be1 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 ccd9b839849600b1aa3b6cf54f667575a5f2da9d
author ebi-gxa
date Fri, 25 Oct 2019 08:19:50 -0400
parents e541f264fad2
children 378ea34bbf2a
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1:e541f264fad2 2:059f8d2e8be1
9 ln -s '${input_obj_file}' input.h5 && 9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-normalise-data 10 PYTHONIOENCODING=utf-8 scanpy-normalise-data
11 --normalize-to ${scale_factor} 11 --normalize-to ${scale_factor}
12 --fraction ${fraction} 12 --fraction ${fraction}
13 --save-raw ${save_raw} 13 --save-raw ${save_raw}
14 ${log_transform}
14 @INPUT_OPTS@ 15 @INPUT_OPTS@
15 @OUTPUT_OPTS@ 16 @OUTPUT_OPTS@
16 ]]></command> 17 ]]></command>
17 18
18 <inputs> 19 <inputs>
21 <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0" 22 <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0"
22 label="Target number to normalise to" help="Aimed counts per cell after normalisation."/> 23 label="Target number to normalise to" help="Aimed counts per cell after normalisation."/>
23 <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1" 24 <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1"
24 label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts" 25 label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts"
25 help="Only non-excluded genes will sum up the target number."/> 26 help="Only non-excluded genes will sum up the target number."/>
27 <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-tranform" checked="True"
28 label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/>
26 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true" 29 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true"
27 label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/> 30 label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/>
28 <expand macro="export_mtx_params"/> 31 <expand macro="export_mtx_params"/>
29 </inputs> 32 </inputs>
30 33