comparison scanpy-normalise-data.xml @ 2:059f8d2e8be1 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ccd9b839849600b1aa3b6cf54f667575a5f2da9d

1:e541f264fad2

ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-normalise-data
    --normalize-to ${scale_factor}
    --fraction ${fraction}
    --save-raw ${save_raw}
    @INPUT_OPTS@
    @OUTPUT_OPTS@
]]></command>

  <inputs>

    <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0"
           label="Target number to normalise to" help="Aimed counts per cell after normalisation."/>
    <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1"
           label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts"
           help="Only non-excluded genes will sum up the target number."/>
    <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true"
           label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/>
    <expand macro="export_mtx_params"/>
  </inputs>

2:059f8d2e8be1

ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-normalise-data
    --normalize-to ${scale_factor}
    --fraction ${fraction}
    --save-raw ${save_raw}
    ${log_transform}
    @INPUT_OPTS@
    @OUTPUT_OPTS@
]]></command>

  <inputs>

    <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0"
           label="Target number to normalise to" help="Aimed counts per cell after normalisation."/>
    <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1"
           label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts"
           help="Only non-excluded genes will sum up the target number."/>
    <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-tranform" checked="True" 
           label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/>
    <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true"
           label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/>
    <expand macro="export_mtx_params"/>
  </inputs>