Mercurial > repos > computational-metabolomics > dimspy_missing_values_sample_filter
comparison missing_values_sample_filter.xml @ 0:91441e41cc3d draft
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
author | computational-metabolomics |
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date | Sat, 11 Apr 2020 16:47:00 -0400 |
parents | |
children | 2cf12cd2c53a |
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1 <tool id="dimspy_missing_values_sample_filter" name="Missing Values Sample Filter" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@"> | |
2 <description> - Remove samples with a high percentage of missing values</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"> | |
8 <![CDATA[ | |
9 dimspy mv-sample-filter | |
10 --input '$hdf5_file_in' | |
11 --output '$hdf5_file_out' | |
12 --max-fraction $max_fraction | |
13 && | |
14 dimspy create-sample-list | |
15 --input '$hdf5_file_out' | |
16 --output '$samplelist' | |
17 --delimiter tab | |
18 #if $hdf5_to_txt.standard | |
19 && | |
20 @HDF5_PM_TO_TXT@ | |
21 #end if | |
22 #if $hdf5_to_txt.comprehensive | |
23 && | |
24 @HDF5_PM_TO_TXT_COMPREHENSIVE@ | |
25 #end if | |
26 ]]> | |
27 </command> | |
28 <inputs> | |
29 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peak Intensity Matrix (HDF5 file)" help="" /> | |
30 <param name="max_fraction" argument="--max-fraction" type="float" min="0" max="1.0" value="0.8" label="Maximum percentage of missing values." help="" /> | |
31 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" label="" help=""/> | |
32 <expand macro="hdf5_pm_to_txt" /> | |
33 </inputs> | |
34 <outputs> | |
35 <expand macro="outputs_peak_intensity_matrix" /> | |
36 <data name="samplelist" format="tsv" label="${tool.name} on ${on_string}: Sample Metadata (updated)" /> | |
37 </outputs> | |
38 <tests> | |
39 <test> | |
40 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/> | |
41 <param name="max_fraction" value="0.8"/> | |
42 <param name="delimiter" value="tab"/> | |
43 <conditional name="hdf5_to_txt"> | |
44 <param name="standard" value="True"/> | |
45 <param name="comprehensive" value="False"/> | |
46 <param name="representation_samples" value="rows"/> | |
47 <param name="matrix_attr" value="intensity"/> | |
48 </conditional> | |
49 <output name="hdf5_file_out" file="pm_as_bf_sf_mv.h5" ftype="h5" compare="sim_size"/> | |
50 <output name="matrix_file_out" file="peak_matrix_as_bf_sf_mv.txt" ftype="tsv"/> | |
51 <output name="samplelist" file="sample_list_after_mv_filter.txt" ftype="tsv"/> | |
52 </test> | |
53 </tests> | |
54 <help> | |
55 ---------------------------- | |
56 Missing Values Sample Filter | |
57 ---------------------------- | |
58 | |
59 .. | |
60 | |
61 --------------------------------------------- | |
62 | |
63 Description | |
64 ----------- | |
65 | |
66 Standard DIMS processing workflow: Process Scans -> Replicate Filter -> Align Samples -> **[Missing values sample filter]** -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics | |
67 | |
68 | | |
69 | |
70 This tool is used to remove study samples with greater-than a user-defined “Maximum percentage of missing values” from the peak intensity matrix. A missing value is defined as the absence of a recorded peak intensity value for a specific mass spectral peak, in a specific study sample. | |
71 | |
72 Samples with large numbers of missing values are often observed where a failed mass spectral acquisition has occurred, the reasons for which are many and diverse. | |
73 | |
74 --------------------------------------------- | |
75 | |
76 Parameters | |
77 ---------- | |
78 | |
79 **Peak Intensity Matrix (HDF5 file)** (REQUIRED) - for routine usage, the input peak intensity matrix should be that generated from the 'Align samples' tool. | |
80 | |
81 **Maximum percentage of missing values** (REQUIRED; default = 0.8) - a numeric value ranging from 0 to 1 (decimal representation of percentage), where: | |
82 | |
83 - A value of 0 (i.e. 0%) corresponds to a very harsh filtering procedure, in which only those samples with zero missing values are retained in the output peak matrix. | |
84 | |
85 - A value of 1 (i.e. 100%) corresponds to a very liberal filtering procedure, in which samples with as many as 100% missing values will be retained in the output peak matrix. | |
86 | |
87 | | |
88 | |
89 @help_options_addtional_output@ | |
90 | |
91 | | |
92 | |
93 --------------------------------------------- | |
94 | |
95 Output file(s) | |
96 -------------- | |
97 | |
98 **IMPORTANT** - in all outputs except for the (optional) comprehensive output, if a sample had greater-than the user defined maximum percentage of missing values, then this sample is removed from the output peak matrix. | |
99 | |
100 | |
101 @help_outputs_matrix@ | |
102 | |
103 --------------------------------------------- | |
104 | |
105 @github_developers_contributors@ | |
106 @license@ | |
107 </help> | |
108 <expand macro="citations" /> | |
109 </tool> | |
110 |