Mercurial > repos > ebi-gxa > scanpy_normalise_data

annotate scanpy-normalise-data.xml @ 0:19805a556cd6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
author ebi-gxa
date Wed, 13 Mar 2019 11:49:12 -0400
parents
children 5704635cef67
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
1 <?xml version="1.0" encoding="utf-8"?>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
2 <tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy0">
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
3 <description>to make all cells having the same total expression</description>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
4 <macros>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
5 <import>scanpy_macros.xml</import>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
6 </macros>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
7 <expand macro="requirements"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
9 ln -s '${input_obj_file}' input.h5 &&
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
10 PYTHONIOENCODING=utf-8 scanpy-normalise-data.py
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
11 -i input.h5
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
12 -f '${input_format}'
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
13 -o output.h5
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
14 -F '${output_format}'
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
15 -s '${scale_factor}'
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
16 #if $save_raw
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
17 '${save_raw}'
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
18 #end if
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
19 ]]></command>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
20
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
21 <inputs>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
22 <expand macro="input_object_params"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
23 <expand macro="output_object_params"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
24 <param name="scale_factor" argument="--scale-factor" type="float" value="1e4" label="Target number to normalise to"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
25 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="--save-raw" falsevalue="" checked="true" label="Save pre-normalised data"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
26 </inputs>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
27
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
28 <outputs>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
29 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Normalized data" />
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
30 </outputs>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
31
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
32 <tests>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
33 <test>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
34 <param name="input_obj_file" value="filter_genes.h5"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
35 <param name="input_format" value="anndata"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
36 <param name="output_format" value="anndata"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
37 <param name="scale_factor" value="1e4"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
38 <param name="save_raw" value="false"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
39 <output name="output_h5" file="normalise_data.h5" ftype="h5" compare="sim_size"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
40 </test>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
41 </tests>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
42
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
43 <help><![CDATA[
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
44 =========================================================
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
45 Normalize total counts per cell (`pp.normalize_per_cell`)
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
46 =========================================================
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
47
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
48 Normalize each cell by total counts over all genes, so that every cell has
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
49 the same total count after normalization.
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
50
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
51 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
52
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
53 @HELP@
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
54
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
55 @VERSION_HISTORY@
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
56 ]]></help>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
57 <expand macro="citations"/>
19805a556cd6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
ebi-gxa
parents:
diff changeset
58 </tool>