Mercurial > repos > iuc > scanpy_normalize

comparison normalize.xml @ 12:94c19fb1281c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
author iuc
date Fri, 17 Nov 2023 09:16:03 +0000
parents c9cb76cf8d6c
children 7b9fafe32c86
comparison
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11:c9cb76cf8d6c 12:94c19fb1281c
1 <tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" profile="@profile@"> 1 <tool id="scanpy_normalize" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
2 <description>with scanpy</description> 2 <description>with scanpy</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
15 @CMD_read_inputs@ 15 @CMD_read_inputs@
16 16
17 #if $method.method == "pp.normalize_total" 17 #if $method.method == "pp.normalize_total"
18 sc.pp.normalize_total( 18 sc.pp.normalize_total(
19 adata, 19 adata,
20 #if str($method.target_sum)!= '' 20 #if str($method.target_sum) != ''
21 target_sum=$method.target_sum, 21 target_sum=$method.target_sum,
22 #end if 22 #end if
23 exclude_highly_expressed=$method.exclude_highly_expressed.exclude_highly_expressed, 23 exclude_highly_expressed=$method.exclude_highly_expressed.exclude_highly_expressed,
24 #if $method.exclude_highly_expressed.exclude_highly_expressed == "True" 24 #if $method.exclude_highly_expressed.exclude_highly_expressed == "True"
25 max_fraction=$method.exclude_highly_expressed.max_fraction, 25 max_fraction=$method.exclude_highly_expressed.max_fraction,
26 #end if 26 #end if
27 #if str($method.key_added) != '' 27 #if $method.key_added
28 key_added='$method.key_added', 28 key_added='$method.key_added',
29 #end if 29 #end if
30 #if str($method.layers) != '' 30 #if $method.layers
31 #if str($method.layers) != 'all' 31 #if str($method.layers) != 'all'
32 layers[str(x.strip()) for x in str($method.layers).split(',')], 32 layers[str(x.strip()) for x in str($method.layers).split(',')],
33 #else 33 #else
34 layers='$method.layers', 34 layers='$method.layers',
35 #end if 35 #end if