Mercurial > repos > iuc > scater_filter
annotate scater-filter.xml @ 1:b7ea9f09c02f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
author | iuc |
---|---|
date | Tue, 03 Sep 2019 14:27:39 -0400 |
parents | e6ca62ac65c6 |
children | 7a365ec81b52 |
rev | line source |
---|---|
0
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
1 <tool id="scater_filter" name="Scater: filter SCE" version="@TOOL_VERSION@"> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
2 <description>with user-defined parameters or PCA</description> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
3 <macros> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
5 </macros> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
6 <expand macro="requirements"> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
7 <requirement type="package" version="2.0.9">r-mvoutlier</requirement> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
8 </expand> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
9 <command detect_errors="exit_code"><![CDATA[ |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
10 #if $filter_type.filter_type_selector == 'manual': |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
11 Rscript '$__tool_directory__/scater-manual-filter.R' |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
12 -i '$input_loom' |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
13 #if str($filter_type.detection_limit): |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
14 --detection-limit ${filter_type.detection_limit} |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
15 #end if |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
16 #if str($filter_type.library_size): |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
17 --library-size ${filter_type.library_size} |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
18 #end if |
1
b7ea9f09c02f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
|
19 #if str($filter_type.expressed_genes): |
b7ea9f09c02f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
|
20 --expressed-genes ${filter_type.expressed_genes} |
b7ea9f09c02f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
|
21 #end if |
0
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
22 #if str($filter_type.percent_counts_MT): |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
23 --percent-counts-MT ${filter_type.percent_counts_MT} |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
24 #end if |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
25 #else: |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
26 Rscript '$__tool_directory__/scater-pca-filter.R' |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
27 -i '$input_loom' |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
28 #end if |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
29 -o '$output_loom' |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
30 ]]></command> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
31 <inputs> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
32 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
33 <conditional name="filter_type"> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
34 <param name="filter_type_selector" type="select" label="Type of filter"> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
35 <option value="manual">manual</option> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
36 <option value="pca">PCA</option> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
37 </param> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
38 <when value="manual"> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
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" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
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" /> |
1
b7ea9f09c02f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
|
41 <param name="expressed_genes" argument="--expressed-genes" type="integer" optional="true" label="Minimum number of expressed genes to filter cells on" /> |
0
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
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" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
43 </when> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
44 <when value="pca" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
45 </conditional> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
46 </inputs> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
47 <outputs> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
48 <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
49 </outputs> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
50 <tests> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
51 <test> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
52 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
53 <param name="filter_type_selector" value="manual" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
54 <param name="detection_limit" value="4" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
55 <param name="library_size" value="100000" /> |
1
b7ea9f09c02f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
|
56 <param name="expressed_genes" value="400" /> |
0
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
57 <param name="percent_counts_MT" value="33.0" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
58 <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
59 </test> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
60 <test> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
61 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
62 <param name="filter_type_selector" value="pca" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
63 <output name="output_loom" file="scater_pca_filtered.loom" compare="sim_size" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
64 </test> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
65 </tests> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
66 <help><![CDATA[ |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
67 Filter a SingleCellLoomExperiment object with Scater using one of the following methods: |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
68 |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
69 - user-defined parameters |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
70 - PCA to automatically removes outliers. |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
71 ]]></help> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
72 <expand macro="citations" /> |
e6ca62ac65c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
|
73 </tool> |