Mercurial > repos > iuc > scanpy_normalize

comparison normalize.xml @ 3:d7ea9b5e6df1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
author iuc
date Thu, 12 Dec 2019 09:27:00 -0500
parents 8e0f141c8c66
children ec32793ce1dd
comparison
equal deleted inserted replaced
2:8e0f141c8c66 3:d7ea9b5e6df1
21 #end if 21 #end if
22 exclude_highly_expressed=$method.exclude_highly_expressed.exclude_highly_expressed, 22 exclude_highly_expressed=$method.exclude_highly_expressed.exclude_highly_expressed,
23 #if $method.exclude_highly_expressed.exclude_highly_expressed == "True" 23 #if $method.exclude_highly_expressed.exclude_highly_expressed == "True"
24 max_fraction=$method.exclude_highly_expressed.max_fraction, 24 max_fraction=$method.exclude_highly_expressed.max_fraction,
25 #end if 25 #end if
26 #if str($method.key_added) != ''
26 key_added='$method.key_added', 27 key_added='$method.key_added',
27 #if str($method.layers) != 'all' 28 #end if
29 #if str($method.layers) != ''
30 #if str($method.layers) != 'all'
28 layers[str(x.strip()) for x in str($method.layers).split(',')], 31 layers[str(x.strip()) for x in str($method.layers).split(',')],
29 #else 32 #else
30 layers='$method.layers', 33 layers='$method.layers',
34 #end if
31 #end if 35 #end if
32 #if str($method.layer_norm) != "None" 36 #if str($method.layer_norm) != "None"
33 layer_norm='$method.layer_norm', 37 layer_norm='$method.layer_norm',
34 #end if 38 #end if
35 inplace=True) 39 inplace=True)
68 </configfiles> 72 </configfiles>
69 <inputs> 73 <inputs>
70 <expand macro="inputs_anndata"/> 74 <expand macro="inputs_anndata"/>
71 <conditional name="method"> 75 <conditional name="method">
72 <param argument="method" type="select" label="Method used for normalization"> 76 <param argument="method" type="select" label="Method used for normalization">
73 <option value="pp.normalize_total">Normalize counts per cell, using `pp.normalize_total`</option> 77 <option value="pp.normalize_total">Normalize counts per cell, using 'pp.normalize_total'</option>
74 <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using `pp.recipe_zheng17`</option> 78 <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using 'pp.recipe_zheng17'</option>
75 <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using `pp.recipe_weinreb17`</option> 79 <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using 'pp.recipe_weinreb17'</option>
76 <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using `pp.recipe_seurat`</option> 80 <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using 'pp.recipe_seurat'</option>
77 </param> 81 </param>
78 <when value="pp.normalize_total"> 82 <when value="pp.normalize_total">
79 <param argument="target_sum" type="float" value="" optional="true" 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."/> 83 <param argument="target_sum" type="float" value="" optional="true" 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."/>
80 <conditional name="exclude_highly_expressed"> 84 <conditional name="exclude_highly_expressed">
81 <param argument="exclude_highly_expressed" type="select" label="Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell" help=" 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 target_sum"> 85 <param argument="exclude_highly_expressed" type="select" label="Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell" help=" 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 target_sum">
85 <when value="True"> 89 <when value="True">
86 <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."/>
87 </when> 91 </when>
88 <when value="False"/> 92 <when value="False"/>
89 </conditional> 93 </conditional>
90 <param argument="key_added" type="text" value="n_counts" 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=""/>
91 <param argument="layers" type="text" value="all" label="List of layers to normalize" help="'All' will normalize all layers. The list should be comma-separated."/> 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."/>
92 <param argument="layer_norm" type="select" label="How to normalize layers?"> 96 <param argument="layer_norm" type="select" label="How to normalize layers?">
93 <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> 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>
94 <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option> 98 <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option>
95 <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> 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>
96 </param> 100 </param>