Mercurial > repos > ebi-gxa > scanpy_scale_data
comparison scanpy-scale-data.xml @ 1:9acb5f068e6b draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
author | ebi-gxa |
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date | Mon, 16 Sep 2019 08:14:52 -0400 |
parents | 96b851e96dd0 |
children | c23efca79651 |
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0:96b851e96dd0 | 1:9acb5f068e6b |
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1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
2 <tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy1"> | 2 <tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy0"> |
3 <description>to make expression variance the same for all genes</description> | 3 <description>to make expression variance the same for all genes</description> |
4 <macros> | 4 <macros> |
5 <import>scanpy_macros.xml</import> | 5 <import>scanpy_macros2.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 ln -s '${input_obj_file}' input.h5 && | 9 ln -s '${input_obj_file}' input.h5 && |
10 PYTHONIOENCODING=utf-8 scanpy-scale-data.py | 10 PYTHONIOENCODING=utf-8 scanpy-scale-data |
11 -i input.h5 | |
12 -f '${input_format}' | |
13 -o output.h5 | |
14 -F '${output_format}' | |
15 #if $scale_max | 11 #if $scale_max |
16 -x '${scale_max}' | 12 --max-value '${scale_max}' |
17 #end if | 13 #end if |
18 #if $var_to_regress | 14 ${zero_center} |
19 -V '${var_to_regress}' | 15 @INPUT_OPTS@ |
20 #end if | 16 @OUTPUT_OPTS@ |
21 #if $do_log | |
22 --do-log | |
23 #end if | |
24 #if $zero_center | |
25 --zero-center | |
26 #end if | |
27 ]]></command> | 17 ]]></command> |
28 | 18 |
29 <inputs> | 19 <inputs> |
30 <expand macro="input_object_params"/> | 20 <expand macro="input_object_params"/> |
31 <expand macro="output_object_params"/> | 21 <expand macro="output_object_params"/> |
32 <param name="do_log" argument="--do-log" type="boolean" checked="true" label="Do log(x+1) transformation"/> | 22 <param name="zero_center" type="boolean" checked="true" truevalue="" falsevalue="--no-zero-center" |
33 <param name="zero_center" argument="--zero-center" type="boolean" checked="true" label="Zero center data before scaling"/> | 23 label="Zero center data before scaling"/> |
34 <param name="var_to_regress" argument="--var-to-regress" type="text" optional="true" label="Variable(s) to regress out"> | 24 <param name="scale_max" argument="--max-value" type="float" min="0" optional="true" label="Truncate to this value after scaling"/> |
35 <option value="n_counts">n_counts</option> | |
36 </param> | |
37 <param name="scale_max" argument="--scale-max" type="float" optional="true" label="Truncate to this value after scaling"/> | |
38 </inputs> | 25 </inputs> |
39 | 26 |
40 <outputs> | 27 <outputs> |
41 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/> | 28 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/> |
42 </outputs> | 29 </outputs> |
44 <tests> | 31 <tests> |
45 <test> | 32 <test> |
46 <param name="input_obj_file" value="find_variable_genes.h5"/> | 33 <param name="input_obj_file" value="find_variable_genes.h5"/> |
47 <param name="input_format" value="anndata"/> | 34 <param name="input_format" value="anndata"/> |
48 <param name="output_format" value="anndata"/> | 35 <param name="output_format" value="anndata"/> |
49 <param name="do_log" value="true"/> | |
50 <param name="zero_center" value="true"/> | 36 <param name="zero_center" value="true"/> |
51 <param name="scale_max" value="10"/> | 37 <param name="scale_max" value="10"/> |
52 <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/> | 38 <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/> |
53 </test> | 39 </test> |
54 </tests> | 40 </tests> |
56 <help><![CDATA[ | 42 <help><![CDATA[ |
57 .. class:: infomark | 43 .. class:: infomark |
58 | 44 |
59 **What it does** | 45 **What it does** |
60 | 46 |
61 Scale data to unit variance and zero mean (`pp.scale`) | 47 Scale data to unit variance and (optionally) zero mean (`scanpy.pp.scale`) |
62 Regress out unwanted sources of variation (`pp.regress_out`) | |
63 | |
64 Regress out unwanted sources of variation, using simple linear regression. This is | |
65 inspired by Seurat's `regressOut` function in R. | |
66 | 48 |
67 @HELP@ | 49 @HELP@ |
68 | 50 |
69 @VERSION_HISTORY@ | 51 @VERSION_HISTORY@ |
70 ]]></help> | 52 ]]></help> |