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comparison scater-filter.xml @ 0:eca7cdc36e1e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author iuc
date Thu, 18 Jul 2019 11:09:31 -0400
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children f15110ba3089
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-1:000000000000 0:eca7cdc36e1e
1 <tool id="scater_filter" name="Scater: filter SCE" version="@TOOL_VERSION@">
2 <description>with user-defined parameters or PCA</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="2.0.9">r-mvoutlier</requirement>
8 </expand>
9 <command detect_errors="exit_code"><![CDATA[
10 #if $filter_type.filter_type_selector == 'manual':
11 Rscript '$__tool_directory__/scater-manual-filter.R'
12 -i '$input_loom'
13 #if str($filter_type.detection_limit):
14 --detection-limit ${filter_type.detection_limit}
15 #end if
16 #if str($filter_type.library_size):
17 --library-size ${filter_type.library_size}
18 #end if
19 #if str($filter_type.percent_counts_MT):
20 --percent-counts-MT ${filter_type.percent_counts_MT}
21 #end if
22 #else:
23 Rscript '$__tool_directory__/scater-pca-filter.R'
24 -i '$input_loom'
25 #end if
26 -o '$output_loom'
27 ]]></command>
28 <inputs>
29 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
30 <conditional name="filter_type">
31 <param name="filter_type_selector" type="select" label="Type of filter">
32 <option value="manual">manual</option>
33 <option value="pca">PCA</option>
34 </param>
35 <when value="manual">
36 <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" />
37 <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" />
38 <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" />
39 </when>
40 <when value="pca" />
41 </conditional>
42 </inputs>
43 <outputs>
44 <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
45 </outputs>
46 <tests>
47 <test>
48 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
49 <param name="filter_type_selector" value="manual" />
50 <param name="detection_limit" value="4" />
51 <param name="library_size" value="100000" />
52 <param name="percent_counts_MT" value="33.0" />
53 <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" />
54 </test>
55 <test>
56 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
57 <param name="filter_type_selector" value="pca" />
58 <output name="output_loom" file="scater_pca_filtered.loom" compare="sim_size" />
59 </test>
60 </tests>
61 <help><![CDATA[
62 Filter a SingleCellLoomExperiment object with Scater using one of the following methods:
63
64 - user-defined parameters
65 - PCA to automatically removes outliers.
66 ]]></help>
67 <expand macro="citations" />
68 </tool>