Mercurial > repos > ebi-gxa > seurat_normalise_data
annotate seurat_normalise_data.xml @ 6:3f49bc9c9213 draft default tip
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author | ebi-gxa |
---|---|
date | Sat, 02 Mar 2024 10:42:30 +0000 |
parents | a835b38e389f |
children |
rev | line source |
---|---|
5
a835b38e389f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
4
diff
changeset
|
1 <tool id="seurat_normalise_data" name="Seurat NormaliseData" profile="18.01" version="@SEURAT_VERSION@+galaxy0"> |
0
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
2 <description>normalise data</description> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
3 <macros> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
4 <import>seurat_macros.xml</import> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
5 </macros> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
6 <expand macro="requirements" /> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
7 <expand macro="version" /> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
8 <command detect_errors="exit_code"><![CDATA[ |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
9 seurat-normalise-data.R |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
10 |
1
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
11 @INPUT_OBJECT@ |
0
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
12 #if $norm: |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
13 --normalization-method $norm |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
14 #end if |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
15 #if $assay: |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
16 --assay-type '$assay' |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
17 #end if |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
18 #if $scale: |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
19 --scale-factor $scale |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
20 #end if |
1
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
21 @OUTPUT_OBJECT@ |
0
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
22 ]]></command> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
23 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
24 <inputs> |
1
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
25 <expand macro="input_object_params"/> |
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
26 <expand macro="output_object_params"/> |
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
27 <param name="norm" argument="--normalization-method" type="select" optional="True" label="Normalisation method" help = "Method for normalization. Default is log-normalization (LogNormalize). Can be 'CLR' or 'RC' additionally."> |
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
28 <option value="LogNormalize" selected="true">Log Normalise</option> |
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
29 <option value="CLR">CLR</option> |
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
30 <option value="RC">RC</option> |
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
31 </param> |
0
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
32 <param name="assay" argument="--assay-type" type="text" optional="True" label="Assay type" help = "Type of assay to normalize for (default is RNA), but can be changed for multimodal analyses."> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
33 <validator type="regex" message="Please only use letters">^[\(\w\)]+$</validator> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
34 </param> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
35 <param name="scale" argument="--scale-factor" type="integer" optional="True" label="Scale factor" help="Sets the scale factor for cell-level normalization"/> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
36 </inputs> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
37 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
38 <outputs> |
1
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
39 <expand macro="output_files"/> |
0
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
40 </outputs> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
41 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
42 <tests> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
43 <test> |
5
a835b38e389f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
4
diff
changeset
|
44 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells.rds"/> |
a835b38e389f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
4
diff
changeset
|
45 <output name="rds_seurat_file" ftype="rdata"> |
a835b38e389f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
4
diff
changeset
|
46 <assert_contents> |
a835b38e389f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
4
diff
changeset
|
47 <has_size value="2720178" delta="200000"/> |
a835b38e389f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
4
diff
changeset
|
48 </assert_contents> |
a835b38e389f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents:
4
diff
changeset
|
49 </output> |
0
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
50 </test> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
51 </tests> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
52 <help><![CDATA[ |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
53 .. class:: infomark |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
54 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
55 **What it does** |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
56 |
1
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
57 This tool normalises a Seurat RDS object. |
0
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
58 |
1
48174ec556de
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
0
diff
changeset
|
59 @SEURAT_INTRO@ |
0
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
60 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
61 ----- |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
62 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
63 **Inputs** |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
64 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
65 * Seurat RDS object. Possibly the output of Seurat filter cells or Seurat create object. |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
66 * Normalisation method. Method for normalization. Default is log-normalization (LogNormalize). |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
67 * Assay type. Type of assay to normalize for (default is RNA), but can be changed for multimodal analyses. |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
68 * Scale factor. Sets the scale factor for cell-level normalization. Default: 1000 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
69 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
70 ----- |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
71 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
72 **Outputs** |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
73 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
74 * Seurat RDS object with normalised matrix. |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
75 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
76 .. _Seurat: https://www.nature.com/articles/nbt.4096 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
77 .. _Satija Lab: https://satijalab.org/seurat/ |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
78 |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
79 @VERSION_HISTORY@ |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
80 ]]></help> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
81 <expand macro="citations" /> |
619fead82856
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
|
82 </tool> |