Mercurial > repos > ebi-gxa > scanpy_normalise_data

comparison scanpy-normalise-data.xml @ 19:3a4564b9d685 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 12:11:45 +0000
parents 6aa97861fdfd
children 6b97ffba31da
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equal deleted inserted replaced
18:28ab1cdd0cf5 19:3a4564b9d685
19 --key-added '${settings.key_added}' 19 --key-added '${settings.key_added}'
20 #end if 20 #end if
21 #if $settings.exclude.exclude_highly_expressed 21 #if $settings.exclude.exclude_highly_expressed
22 --exclude-highly-expressed --max-fraction '${settings.exclude.max_fraction}' 22 --exclude-highly-expressed --max-fraction '${settings.exclude.max_fraction}'
23 #end if 23 #end if
24 #if $settings.save_raw
25 --save-raw ${settings.save_raw}
26 #end if
27 #end if 24 #end if
28 @INPUT_OPTS@ 25 @INPUT_OPTS@
29 @OUTPUT_OPTS@ 26 @OUTPUT_OPTS@
27 @SAVE_MATRIX_OPTS@
30 @EXPORT_MTX_OPTS@ 28 @EXPORT_MTX_OPTS@
31 ]]></command> 29 ]]></command>
32 30
33 <inputs> 31 <inputs>
34 <expand macro="input_object_params"/> 32 <expand macro="input_object_params"/>
35 <expand macro="output_object_params"/> 33 <expand macro="output_object_params"/>
36 <expand macro="export_mtx_params"/> 34 <expand macro="export_mtx_params"/>
35 <expand macro="save_matrix_params"/>
37 <conditional name="settings"> 36 <conditional name="settings">
38 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> 37 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
39 <when value="true"/> 38 <when value="true"/>
40 <when value="false"> 39 <when value="false">
41 <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0" 40 <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0"
42 label="Target number to normalise to" help="Aimed counts per cell after normalisation."/> 41 label="Target number to normalise to" help="Aimed counts per cell after normalisation."/>
43 <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" checked="True" 42 <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" checked="True"
44 label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/> 43 label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/>
45 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true"
46 label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/>
47 <conditional name="exclude"> 44 <conditional name="exclude">
48 <param name="exclude_highly_expressed" argument="--exclude-highly-expressed" type="boolean" checked="False" 45 <param name="exclude_highly_expressed" argument="--exclude-highly-expressed" type="boolean" checked="False"
49 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."/> 46 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."/>
50 <when value="true"> 47 <when value="true">
51 <param name="max_fraction" argument="--max-fraction" type="float" value="0.05" min="0" max="1" 48 <param name="max_fraction" argument="--max-fraction" type="float" value="0.05" min="0" max="1"