Mercurial > repos > ebi-gxa > scanpy_normalise_data
diff scanpy-normalise-data.xml @ 19:3a4564b9d685 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 |
---|---|
date | Wed, 05 May 2021 12:11:45 +0000 |
parents | 6aa97861fdfd |
children | 6b97ffba31da |
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--- a/scanpy-normalise-data.xml Mon Apr 12 14:43:58 2021 +0000 +++ b/scanpy-normalise-data.xml Wed May 05 12:11:45 2021 +0000 @@ -21,12 +21,10 @@ #if $settings.exclude.exclude_highly_expressed --exclude-highly-expressed --max-fraction '${settings.exclude.max_fraction}' #end if - #if $settings.save_raw - --save-raw ${settings.save_raw} - #end if #end if @INPUT_OPTS@ @OUTPUT_OPTS@ + @SAVE_MATRIX_OPTS@ @EXPORT_MTX_OPTS@ ]]></command> @@ -34,6 +32,7 @@ <expand macro="input_object_params"/> <expand macro="output_object_params"/> <expand macro="export_mtx_params"/> + <expand macro="save_matrix_params"/> <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> @@ -42,8 +41,6 @@ label="Target number to normalise to" help="Aimed counts per cell after normalisation."/> <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" 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."/> <conditional name="exclude"> <param name="exclude_highly_expressed" argument="--exclude-highly-expressed" type="boolean" checked="False" label="Exclude highly expressed genes?" help="Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell. A gene is considered highly expressed, if it has more than max_fraction of the total counts in at least one cell. The not-excluded genes will sum up to the number specified by --normalize-to."/>