Mercurial > repos > ebi-gxa > scanpy_integrate_combat
comparison scanpy-integrate-combat.xml @ 0:2472523c0c50 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author | ebi-gxa |
---|---|
date | Mon, 07 Sep 2020 13:06:34 +0000 |
parents | |
children | aaf4a7a3dd96 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:2472523c0c50 |
---|---|
1 <?xml version="1.0" encoding="utf-8"?> | |
2 <tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> | |
3 <description>adjust expression for variables that might introduce batch effect</description> | |
4 <macros> | |
5 <import>scanpy_macros2.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 #if $batch_key | |
10 ln -s '${input_obj_file}' input.h5 && | |
11 PYTHONIOENCODING=utf-8 scanpy-integrate combat | |
12 --batch-key '${batch_key}' | |
13 #if $batch_layer | |
14 --batch-layer '${batch_layer}' | |
15 #end if | |
16 #if $covariates | |
17 --covariates '${$covariates}' | |
18 #end if | |
19 #if $key_added | |
20 --key-added '${key_added}' | |
21 #end if | |
22 @INPUT_OPTS@ | |
23 @OUTPUT_OPTS@ | |
24 #else | |
25 echo "No batch variables passed, simply passing original input as output unchanged."; | |
26 cp '${input_obj_file}' '${output_h5}' | |
27 #end if | |
28 ]]></command> | |
29 | |
30 <inputs> | |
31 <expand macro="input_object_params"/> | |
32 <expand macro="output_object_params"/> | |
33 <param name="batch_key" type="text" argument="--batch-key" label="The name of the column in adata.obs that differentiates among experiments/batches."> | |
34 <sanitizer> | |
35 <valid initial="string.printable"/> | |
36 </sanitizer> | |
37 </param> | |
38 <param name="batch_layer" type="text" argument="--batch-layer" label="Layer to batch correct. By default corrects the contents of .X."> | |
39 <sanitizer> | |
40 <valid initial="string.printable"/> | |
41 </sanitizer> | |
42 </param> | |
43 <param name="covariates" argument="--covariates" type="text" label="Comma separated list of additional covariates besides the batch variable such as adjustment variables or biological condition." help="This parameter refers to the design matrix X in Equation 2.1 in [Johnson07] and to the mod argument in the original combat function in the sva R package. Note that not including covariates may introduce bias or lead to the removal of biological signal in unbalanced designs."> | |
44 <sanitizer> | |
45 <valid initial="string.printable"/> | |
46 </sanitizer> | |
47 </param> | |
48 <param name="key_added" argument="--key-added" type="text" optional="true" | |
49 label="Key under which to add the computed results." help="By default a new layer will be created called 'combat', 'combat_{layer}' or 'combat_{layer}_{key_added}' where those parameters were specified. A value of 'X' causes batch-corrected values to overwrite the original content of .X."/> | |
50 </inputs> | |
51 | |
52 <outputs> | |
53 <expand macro="output_data_obj" description="Batch-corrected for ${batch_key}"/> | |
54 </outputs> | |
55 | |
56 <tests> | |
57 <test> | |
58 <param name="input_obj_file" value="find_cluster.h5"/> | |
59 <param name="input_format" value="anndata"/> | |
60 <param name="output_format" value="anndata"/> | |
61 <param name="batch_key" value="louvain"/> | |
62 <output name="output_h5" file="combat.h5" ftype="h5" compare="sim_size"/> | |
63 </test> | |
64 </tests> | |
65 | |
66 <help><![CDATA[ | |
67 .. class:: infomark | |
68 | |
69 **What it does** | |
70 | |
71 Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes. | |
72 | |
73 @HELP@ | |
74 | |
75 @VERSION_HISTORY@ | |
76 ]]></help> | |
77 <expand macro="citations"/> | |
78 </tool> |