Mercurial > repos > ebi-gxa > scanpy_run_pca
comparison scanpy-run-pca.xml @ 1:7798c318e7d7 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 08:12:12 -0400 |
parents | 5063cd7f8c89 |
children | 242cf7e1fd0c |
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0:5063cd7f8c89 | 1:7798c318e7d7 |
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1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
2 <tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy1"> | 2 <tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy0"> |
3 <description>for dimensionality reduction</description> | 3 <description>for dimensionality reduction</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-run-pca.py | 10 PYTHONIOENCODING=utf-8 scanpy-run-pca |
11 -i input.h5 | 11 --n-comps '${n_pcs}' |
12 -f '${input_format}' | 12 #if $run_mode.chunked |
13 -o output.h5 | 13 --chunked |
14 -F '${output_format}' | 14 --chunk-size '${run_mode.chunk_size}' |
15 -n '${n_pcs}' | 15 #else |
16 #if $run_mode.chunked | 16 ${run_mode.zero_center} |
17 -c | 17 #if $run_mode.svd_solver |
18 --chunk-size '${run_mode.chunk_size}' | 18 --svd-solver '${run_mode.svd_solver}' |
19 #else | |
20 #if $run_mode.zero_center | |
21 -z | |
22 #else | |
23 -Z | |
24 #end if | |
25 #if $run_mode.svd_solver | |
26 --svd-solver '${run_mode.svd_solver}' | |
27 #end if | |
28 #if $run_mode.random_seed is not None | |
29 -s '${run_mode.random_seed}' | |
30 #end if | |
31 #end if | 19 #end if |
32 #if $extra_outputs: | 20 #if $run_mode.random_seed is not None |
33 #set extras = ' '.join(['--output-{}-file {}.csv'.format(x, x) for x in str($extra_outputs).split(',')]) | 21 --random-state '${run_mode.random_seed}' |
34 ${extras} | |
35 #end if | 22 #end if |
36 | 23 #end if |
37 @PLOT_OPTS@ | 24 #if $extra_outputs and "embeddings" in str($extra_outputs).split(','): |
25 --export-embedding embeddings.tsv | |
26 #end if | |
27 @INPUT_OPTS@ | |
28 @OUTPUT_OPTS@ | |
38 ]]></command> | 29 ]]></command> |
39 | 30 |
40 <inputs> | 31 <inputs> |
41 <expand macro="input_object_params"/> | 32 <expand macro="input_object_params"/> |
42 <expand macro="output_object_params"/> | 33 <expand macro="output_object_params"/> |
43 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" label="Number of PCs to produce"/> | 34 <param name="n_pcs" argument="--n-comps" type="integer" min="2" value="50" label="Number of PCs to produce"/> |
44 <conditional name="run_mode"> | 35 <conditional name="run_mode"> |
45 <param name="chunked" argument="--chunked" type="boolean" checked="false" label="Perform incremental PCA by chunks"/> | 36 <param name="chunked" argument="--chunked" type="boolean" checked="false" label="Perform incremental PCA by chunks"/> |
46 <when value="true"> | 37 <when value="true"> |
47 <param name="chunk_size" argument="--chunk-size" type="integer" value="0" label="Chunk size"/> | 38 <param name="chunk_size" argument="--chunk-size" type="integer" value="0" label="Chunk size"/> |
48 </when> | 39 </when> |
49 <when value="false"> | 40 <when value="false"> |
50 <param name="zero_center" argument="--zero-center" type="boolean" checked="true" label="Zero center data before scaling"/> | 41 <param name="zero_center" argument="--zero-center" type="boolean" truevalue="" falsevalue="--no-zero-center" checked="true" |
42 label="Zero center data before scaling"/> | |
51 <param name="svd_solver" argument="--svd-solver" type="select" optional="true" label="SVD solver"> | 43 <param name="svd_solver" argument="--svd-solver" type="select" optional="true" label="SVD solver"> |
52 <option value="arpack">ARPACK</option> | 44 <option value="arpack">ARPACK</option> |
53 <option value="randomised">Randomised</option> | 45 <option value="randomized">Randomised</option> |
54 </param> | 46 </param> |
55 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="random_seed for numpy random number generator"/> | 47 <param name="random_seed" argument="--random-state" type="integer" value="0" label="random seed for numpy random number generator"/> |
56 </when> | 48 </when> |
57 </conditional> | 49 </conditional> |
58 | 50 |
59 <param name="extra_outputs" type="select" multiple="true" optional="true" label="Type of output"> | 51 <param name="extra_outputs" type="select" multiple="true" display="checkboxes" optional="true" label="Export extra output"> |
60 <option value="embeddings">PCA embeddings</option> | 52 <option value="embeddings">PCA embeddings</option> |
61 <option value="loadings">PCA loadings</option> | |
62 <option value="stdev">PCs stdev</option> | |
63 <option value="var-ratio">PCs proportion of variance</option> | |
64 </param> | 53 </param> |
65 | 54 |
66 <conditional name="do_plotting"> | |
67 <param name="plot" type="boolean" checked="false" label="Make PCA plot"/> | |
68 <when value="true"> | |
69 <expand macro="output_plot_params"/> | |
70 </when> | |
71 <when value="false"/> | |
72 </conditional> | |
73 </inputs> | 55 </inputs> |
74 | 56 |
75 <outputs> | 57 <outputs> |
76 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: PCA object"/> | 58 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: PCA object"/> |
77 <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: PCA plot"> | 59 <data name="output_embed" format="tsv" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: PCA embeddings"> |
78 <filter>do_plotting['plot']</filter> | |
79 </data> | |
80 <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: PCA embeddings"> | |
81 <filter>extra_outputs and 'embeddings' in extra_outputs.split(',')</filter> | 60 <filter>extra_outputs and 'embeddings' in extra_outputs.split(',')</filter> |
82 </data> | |
83 <data name="output_load" format="csv" from_work_dir="loadings.csv" label="${tool.name} on ${on_string}: PCA loadings"> | |
84 <filter>extra_outputs and 'loadings' in extra_outputs.split(',')</filter> | |
85 </data> | |
86 <data name="output_stdev" format="csv" from_work_dir="stdev.csv" label="${tool.name} on ${on_string}: PCA stdev"> | |
87 <filter>extra_outputs and 'stdev' in extra_outputs.split(',')</filter> | |
88 </data> | |
89 <data name="output_vprop" format="csv" from_work_dir="var-ratio.csv" label="${tool.name} on ${on_string}: PC explained proportion of variance"> | |
90 <filter>extra_outputs and 'var-ratio' in extra_outputs.split(',')</filter> | |
91 </data> | 61 </data> |
92 </outputs> | 62 </outputs> |
93 | 63 |
94 <tests> | 64 <tests> |
95 <test> | 65 <test> |
100 <param name="n_pcs" value="50"/> | 70 <param name="n_pcs" value="50"/> |
101 <param name="zero_center" value="true"/> | 71 <param name="zero_center" value="true"/> |
102 <param name="svd_solver" value="arpack"/> | 72 <param name="svd_solver" value="arpack"/> |
103 <param name="random_seed" value="0"/> | 73 <param name="random_seed" value="0"/> |
104 <param name="chunked" value="false"/> | 74 <param name="chunked" value="false"/> |
105 <param name="plot" value="true"/> | |
106 <param name="color_by" value="n_genes"/> | |
107 <output name="output_h5" file="run_pca.h5" ftype="h5" compare="sim_size"/> | 75 <output name="output_h5" file="run_pca.h5" ftype="h5" compare="sim_size"/> |
108 <output name="output_png" file="run_pca.png" ftype="png" compare="sim_size"/> | |
109 <output name="output_embed" file="run_pca.embeddings.csv" ftype="csv" compare="sim_size"> | 76 <output name="output_embed" file="run_pca.embeddings.csv" ftype="csv" compare="sim_size"> |
110 <assert_contents> | 77 <assert_contents> |
111 <has_n_columns n="50" sep=","/> | 78 <has_n_columns n="50" sep=","/> |
112 </assert_contents> | 79 </assert_contents> |
113 </output> | 80 </output> |
114 </test> | 81 </test> |
115 </tests> | 82 </tests> |
116 | 83 |
117 <help><![CDATA[ | 84 <help><![CDATA[ |
118 ======================================================================================================= | 85 ================================================================================ |
119 Computes PCA (principal component analysis) coordinates, loadings and variance decomposition (`tl.pca`) | 86 Dimensionality reduction by PCA (principal component analysis) (`scanpy.pp.pca`) |
120 ======================================================================================================= | 87 ================================================================================ |
121 | 88 |
122 It uses the implementation of *scikit-learn*. | 89 It uses the implementation of *scikit-learn*. |
123 | 90 |
124 @HELP@ | 91 @HELP@ |
125 | 92 |