Mercurial > repos > recetox > recetox_aplcms_generate_feature_table
annotate recetox_aplcms_generate_feature_table.xml @ 5:702a849c1e0e draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
author | recetox |
---|---|
date | Thu, 22 Jun 2023 11:45:10 +0000 |
parents | 477b5144a422 |
children | e7305ba0dd38 |
rev | line source |
---|---|
5
702a849c1e0e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents:
3
diff
changeset
|
1 <tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy2" profile="21.09"> |
0
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
2 <description>generate feature table from noise-removed HRMS profile data</description> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
3 <macros> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
4 <import>macros.xml</import> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
5 <import>help.xml</import> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
6 </macros> |
5
702a849c1e0e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents:
3
diff
changeset
|
7 <edam_operations> |
702a849c1e0e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents:
3
diff
changeset
|
8 <edam_operation>operation_3215</edam_operation> |
702a849c1e0e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents:
3
diff
changeset
|
9 <edam_operation>operation_3799</edam_operation> |
702a849c1e0e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents:
3
diff
changeset
|
10 </edam_operations> |
702a849c1e0e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents:
3
diff
changeset
|
11 <expand macro="annotation"/> |
0
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
12 <expand macro="creator"/> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
13 <expand macro="requirements"/> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
14 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
15 <command detect_errors="aggressive"><![CDATA[ |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
16 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
17 ]]></command> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
18 <configfiles> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
19 <configfile name="run_script"><![CDATA[ |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
20 profile <- load_data_from_parquet_file('$profile') |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
21 sample_name <- load_sample_name(profile) |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
22 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
23 if(is.na(sample_name)) { |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
24 message("The file does not contain sample name.") |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
25 } |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
26 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
27 feature_table <- prof.to.features( |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
28 profile = profile, |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
29 bandwidth = $bandwidth, |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
30 #if $min_bandwidth: |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
31 min_bandwidth = $min_bandwidth, |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
32 #else: |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
33 min_bandwidth = NA, |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
34 #end if |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
35 #if $max_bandwidth: |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
36 max_bandwidth = $max_bandwidth, |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
37 #else: |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
38 max_bandwidth = NA, |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
39 #end if |
1
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
40 #if $advanced.sd_cut.sd_cut_bounds == "FALSE": |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
41 sd_cut = c($advanced.sd_cut.sd_cut_min, $advanced.sd_cut.sd_cut_max), |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
42 #else |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
43 sd_cut = c(0, Inf), |
0
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
44 #end if |
1
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
45 sigma_ratio_lim = determine_sigma_ratios($advanced.shape_model.sigma_ratio_lim_min, $advanced.shape_model.sigma_ratio_lim_max), |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
46 shape_model = "bi-Gaussian", |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
47 peak_estim_method = "$advanced.peak_estim.peak_estim_method", |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
48 component_eliminate = $advanced.component_eliminate, |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
49 #if $advanced.peak_estim.peak_estim_method == "moment": |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
50 moment_power = $advanced.peak_estim.moment_power, |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
51 #else |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
52 moment_power = 1, |
e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents:
0
diff
changeset
|
53 #end if |
0
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
54 BIC_factor = $BIC_factor, |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
55 do.plot = FALSE |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
56 ) |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
57 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
58 feature_table <- save_sample_name(feature_table, sample_name) |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
59 save_data_as_parquet_file(feature_table, '$output_file') |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
60 ]]></configfile> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
61 </configfiles> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
62 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
63 <inputs> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
64 <param label="Input profile data" name="profile" type="data" format="parquet" |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
65 help="Mass spectrometry profile data." /> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
66 <expand macro="bandwidth_params"/> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
67 <expand macro="generate_feature_table_params"/> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
68 </inputs> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
69 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
70 <outputs> |
3
477b5144a422
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 505c3374a3e1e9aa450fcb752f2b8f87558fedbb
recetox
parents:
1
diff
changeset
|
71 <data label="${($profile.element_identifier).rsplit('.',1)[0]}.parquet" name="output_file" format="parquet" /> |
0
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
72 </outputs> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
73 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
74 <tests> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
75 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
76 </tests> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
77 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
78 <help> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
79 <![CDATA[ |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
80 @GENERATE_FEATURE_TABLE_HELP@ |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
81 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
82 @GENERAL_HELP@ |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
83 ]]> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
84 </help> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
85 |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
86 <expand macro="citations"/> |
2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff
changeset
|
87 </tool> |