Mercurial > repos > iuc > scanpy_normalize

comparison normalize.xml @ 7:a407e7f8bdc1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
author iuc
date Wed, 20 May 2020 16:09:36 -0400
parents 3bcd5445cd7a
children 5342ce58cd1e
comparison
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6:3bcd5445cd7a 7:a407e7f8bdc1
89 <when value="True"> 89 <when value="True">
90 <param argument="max_fraction" type="float" value="0.05" label="Target sum" help="If not provided, after normalization, each observation (cell) has a total count equal to the median of the total counts (cells) before normalization."/> 90 <param argument="max_fraction" type="float" value="0.05" label="Target sum" help="If not provided, after normalization, each observation (cell) has a total count equal to the median of the total counts (cells) before normalization."/>
91 </when> 91 </when>
92 <when value="False"/> 92 <when value="False"/>
93 </conditional> 93 </conditional>
94 <param argument="key_added" type="text" value="" optional="true" label="Name of the field in 'adata.obs' where the normalization factor is stored" help=""/> 94 <param argument="key_added" type="text" value="" optional="true" label="Name of the field in 'adata.obs' where the normalization factor is stored" help="">
95 <param argument="layers" type="text" value="" optional="true" label="List of layers to normalize" help="'All' will normalize all layers. The list should be comma-separated."/> 95 <expand macro="sanitize_query" />
96 </param>
97 <param argument="layers" type="text" value="" optional="true" label="List of layers to normalize" help="'All' will normalize all layers. The list should be comma-separated.">
98 <expand macro="sanitize_query" />
99 </param>
96 <param argument="layer_norm" type="select" label="How to normalize layers?"> 100 <param argument="layer_norm" type="select" label="How to normalize layers?">
97 <option value="None">None: after normalization, for each layer in layers each cell has a total count equal to the median of the median of the total counts (cells) before normalization of the layer.</option> 101 <option value="None">None: after normalization, for each layer in layers each cell has a total count equal to the median of the median of the total counts (cells) before normalization of the layer.</option>
98 <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option> 102 <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option>
99 <option value="X">X: for each layer in layers each cell has a total count equal to the median of total counts for observations (cells) of adata.X before normalization.</option> 103 <option value="X">X: for each layer in layers each cell has a total count equal to the median of total counts for observations (cells) of adata.X before normalization.</option>
100 </param> 104 </param>