Mercurial > repos > ebi-gxa > scanpy_normalise_data

comparison scanpy-normalise-data.xml @ 13:6aa97861fdfd 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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 13:13:49 +0000
parents a97c37e0309a
children 3a4564b9d685
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12:47c747351d62 13:6aa97861fdfd
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> 2 <tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>to make all cells having the same total expression</description> 3 <description>to make all cells having the same total expression</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 && 9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-normalise-data 10 PYTHONIOENCODING=utf-8 scanpy-normalise-data
11 --normalize-to ${scale_factor} 11 #if not $settings.default
12 --fraction ${fraction} 12 #if not $settings.log_transform
13 --save-raw ${save_raw} 13 ${settings.log_transform}
14 ${log_transform} 14 #end if
15 #if $settings.scale_factor
16 --normalize-to '${settings.scale_factor}'
17 #end if
18 #if $settings.key_added
19 --key-added '${settings.key_added}'
20 #end if
21 #if $settings.exclude.exclude_highly_expressed
22 --exclude-highly-expressed --max-fraction '${settings.exclude.max_fraction}'
23 #end if
24 #if $settings.save_raw
25 --save-raw ${settings.save_raw}
26 #end if
27 #end if
15 @INPUT_OPTS@ 28 @INPUT_OPTS@
16 @OUTPUT_OPTS@ 29 @OUTPUT_OPTS@
17 @EXPORT_MTX_OPTS@ 30 @EXPORT_MTX_OPTS@
18 ]]></command> 31 ]]></command>
19 32
20 <inputs> 33 <inputs>
21 <expand macro="input_object_params"/> 34 <expand macro="input_object_params"/>
22 <expand macro="output_object_params"/> 35 <expand macro="output_object_params"/>
23 <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0"
24 label="Target number to normalise to" help="Aimed counts per cell after normalisation."/>
25 <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1"
26 label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts"
27 help="Only non-excluded genes will sum up the target number."/>
28 <param name="log_transform" argument="--no-log-transform" type="boolean" truevalue="" falsevalue="--no-log-transform" checked="True"
29 label="Apply log transform?" help="If enabled, will apply a log transformation following normalisation."/>
30 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true"
31 label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/>
32 <expand macro="export_mtx_params"/> 36 <expand macro="export_mtx_params"/>
37 <conditional name="settings">
38 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
39 <when value="true"/>
40 <when value="false">
41 <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."/>
43 <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."/>
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">
48 <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."/>
50 <when value="true">
51 <param name="max_fraction" argument="--max-fraction" type="float" value="0.05" min="0" max="1"
52 label="Consider cells as highly expressed that have more counts than max_fraction of the original total counts in at least one cell." />
53 </when>
54 </conditional>
55 <param name="layers" argument="--layers" type="text" optional="true"
56 label="Comma-separated list of layers to normalize. Set to 'all' to normalize all layers."/>
57 <param name="layer_norm" type="select" label="How to normalise layers" help="If None, after normalization, for each layer in layers each cell has a total count equal to the median of the counts_per_cell before normalization of the layer. If 'after', for each layer in layers each cell has a total count equal to the value of --normalize-to. If '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." >
58 <option value="" selected="true">None</option>
59 <option value="X">X</option>
60 <option value="after">after</option>
61 </param>
62
63 <param name="key_added" argument="--key-added" type="text" optional="true"
64 label="Name of the field in adata.obs where the normalization factor is stored. Default: don't store."/>
65 </when>
66 </conditional>
33 </inputs> 67 </inputs>
34 68
35 <outputs> 69 <outputs>
36 <expand macro="output_data_obj" description="Normalised data"/> 70 <expand macro="output_data_obj" description="Normalised data"/>
37 <expand macro="export_mtx_outputs"/> 71 <expand macro="export_mtx_outputs"/>