comparison normalize.xml @ 7:a407e7f8bdc1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"

6:3bcd5445cd7a

                    <when value="True">
                        <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."/>
                    </when>
                    <when value="False"/>
                </conditional>
                <param argument="key_added" type="text" value="" optional="true" label="Name of the field in 'adata.obs' where the normalization factor is stored" help=""/>
                <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."/>
                <param argument="layer_norm" type="select" label="How to normalize layers?">
                    <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>
                    <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option>
                    <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>
                </param>

7:a407e7f8bdc1

                    <when value="True">
                        <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."/>
                    </when>
                    <when value="False"/>
                </conditional>
                <param argument="key_added" type="text" value="" optional="true" label="Name of the field in 'adata.obs' where the normalization factor is stored" help="">
                    <expand macro="sanitize_query" />
                </param>
                <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.">
                    <expand macro="sanitize_query" />
                </param>
                <param argument="layer_norm" type="select" label="How to normalize layers?">
                    <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>
                    <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option>
                    <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>
                </param>