Mercurial > repos > iuc > scater_filter
comparison scater-filter.xml @ 0:e6ca62ac65c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author | iuc |
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date | Thu, 18 Jul 2019 11:13:41 -0400 |
parents | |
children | b7ea9f09c02f |
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-1:000000000000 | 0:e6ca62ac65c6 |
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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> |