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comparison scater-filter.xml @ 2:7a365ec81b52 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
author iuc
date Thu, 09 Sep 2021 12:24:17 +0000
parents b7ea9f09c02f
children 652923ce664f
comparison
equal deleted inserted replaced
1:b7ea9f09c02f 2:7a365ec81b52
1 <tool id="scater_filter" name="Scater: filter SCE" version="@TOOL_VERSION@"> 1 <tool id="scater_filter" name="Scater: filter SCE" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>with user-defined parameters or PCA</description> 2 <description>with user-defined parameters or PCA</description>
3 <expand macro="bio_tools"/>
3 <macros> 4 <macros>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 <expand macro="requirements"> 7 <expand macro="requirements">
7 <requirement type="package" version="2.0.9">r-mvoutlier</requirement> 8 <requirement type="package" version="0.93_8">r-robustbase</requirement>
8 </expand> 9 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 #if $filter_type.filter_type_selector == 'manual': 11 #if $filter_type.filter_type_selector == 'manual':
11 Rscript '$__tool_directory__/scater-manual-filter.R' 12 Rscript '$__tool_directory__/scater-manual-filter.R'
12 -i '$input_loom' 13 -i '$input_loom'
14 #if str($filter_type.library_size):
15 --library-size ${filter_type.library_size}
16 #end if
17 #if str($filter_type.percent_counts_MT):
18 --percent-counts-MT ${filter_type.percent_counts_MT}
19 #end if
20 #if str($filter_type.expressed_features):
21 --expressed-features ${filter_type.expressed_features}
22 #end if
13 #if str($filter_type.detection_limit): 23 #if str($filter_type.detection_limit):
14 --detection-limit ${filter_type.detection_limit} 24 --detection-limit ${filter_type.detection_limit}
15 #end if 25 #end if
16 #if str($filter_type.library_size): 26 #if str($filter_type.min_cells_expressed):
17 --library-size ${filter_type.library_size} 27 --min-cells-expressed ${filter_type.min_cells_expressed}
18 #end if
19 #if str($filter_type.expressed_genes):
20 --expressed-genes ${filter_type.expressed_genes}
21 #end if
22 #if str($filter_type.percent_counts_MT):
23 --percent-counts-MT ${filter_type.percent_counts_MT}
24 #end if 28 #end if
25 #else: 29 #else:
26 Rscript '$__tool_directory__/scater-pca-filter.R' 30 Rscript '$__tool_directory__/scater-pca-filter.R'
27 -i '$input_loom' 31 -i '$input_loom'
28 #end if 32 #end if
34 <param name="filter_type_selector" type="select" label="Type of filter"> 38 <param name="filter_type_selector" type="select" label="Type of filter">
35 <option value="manual">manual</option> 39 <option value="manual">manual</option>
36 <option value="pca">PCA</option> 40 <option value="pca">PCA</option>
37 </param> 41 </param>
38 <when value="manual"> 42 <when value="manual">
39 <param name="detection_limit" argument="--detection-limit" type="float" optional="true" label="Number of reads mapped to a gene for it to be counted as expressed" help="Raising this number will raise the stringency and may lower the number of expressed genes" />
40 <param name="library_size" argument="--library-size" type="integer" optional="true" label="Minimum library size (mapped reads) to filter cells on" help="Raising this number will raise the stringency and may lower the number of included cells" /> 43 <param name="library_size" argument="--library-size" type="integer" optional="true" label="Minimum library size (mapped reads) to filter cells on" help="Raising this number will raise the stringency and may lower the number of included cells" />
41 <param name="expressed_genes" argument="--expressed-genes" type="integer" optional="true" label="Minimum number of expressed genes to filter cells on" /> 44 <param name="percent_counts_MT" argument="--percent-counts-MT" type="float" min="0" max="100" optional="true" label="Maximum % of mitochondrial genes expressed per cell" help="Cells that exceed this value will be filtered out" />
42 <param name="percent_counts_MT" argument="--percent-counts-MT" type="float" optional="true" label="Maximum % of mitochondrial genes expressed per cell" help="Cells that exceed this value will be filtered out" /> 45 <param name="expressed_features" type="integer" value="100" optional="true" label="Remove cells that have less than the given number of expressed features" />
46 <param name="detection_limit" argument="--detection-limit" type="float" optional="true" label="Number of reads mapped to a feature above which it to be deemed as expressed" help="Raising this number will raise the stringency and may lower the number of expressed genes" />
47 <param name="min_cells_expressed" argument="---min-cells-expressed" type="integer" optional="true" label="Remove features that occur in less than the given number of cells" help="Features that exceed this value will be filtered out" />
43 </when> 48 </when>
44 <when value="pca" /> 49 <when value="pca" />
45 </conditional> 50 </conditional>
46 </inputs> 51 </inputs>
47 <outputs> 52 <outputs>
51 <test> 56 <test>
52 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> 57 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
53 <param name="filter_type_selector" value="manual" /> 58 <param name="filter_type_selector" value="manual" />
54 <param name="detection_limit" value="4" /> 59 <param name="detection_limit" value="4" />
55 <param name="library_size" value="100000" /> 60 <param name="library_size" value="100000" />
56 <param name="expressed_genes" value="400" />
57 <param name="percent_counts_MT" value="33.0" /> 61 <param name="percent_counts_MT" value="33.0" />
62 <param name="min_cells_expressed" value="3" />
58 <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" /> 63 <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" />
59 </test> 64 </test>
60 <test> 65 <test>
61 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> 66 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
62 <param name="filter_type_selector" value="pca" /> 67 <param name="filter_type_selector" value="pca" />