Mercurial > repos > computational-metabolomics > dimspy_missing_values_sample_filter

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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"
author computational-metabolomics
date Wed, 17 Feb 2021 10:53:54 +0000
parents 2cf12cd2c53a
children
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91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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1 <tool id="dimspy_missing_values_sample_filter" name="Missing Values Sample Filter" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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2 <description> - Remove samples with a high percentage of missing values</description>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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3 <macros>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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4 <import>macros.xml</import>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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5 </macros>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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6 <expand macro="requirements" />
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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7 <command detect_errors="exit_code">
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8 <![CDATA[
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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9 dimspy mv-sample-filter
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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10 --input '$hdf5_file_in'
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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11 --output '$hdf5_file_out'
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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12 --max-fraction $max_fraction
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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13 &&
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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14 dimspy create-sample-list
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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15 --input '$hdf5_file_out'
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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16 --output '$samplelist'
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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17 --delimiter tab
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18 #if $hdf5_to_txt.standard
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19 &&
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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20 @HDF5_PM_TO_TXT@
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21 #end if
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22 #if $hdf5_to_txt.comprehensive
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23 &&
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24 @HDF5_PM_TO_TXT_COMPREHENSIVE@
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25 #end if
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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26 ]]>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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27 </command>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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28 <inputs>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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29 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peak Intensity Matrix (HDF5 file)" help="" />
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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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="" />
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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31 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" label="" help=""/>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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32 <expand macro="hdf5_pm_to_txt" />
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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33 </inputs>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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34 <outputs>
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35 <expand macro="outputs_peak_intensity_matrix" />
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36 <data name="samplelist" format="tsv" label="${tool.name} on ${on_string}: Sample Metadata (updated)" />
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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37 </outputs>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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38 <tests>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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39 <test>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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40 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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41 <param name="max_fraction" value="0.8"/>
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42 <param name="delimiter" value="tab"/>
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43 <conditional name="hdf5_to_txt">
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44 <param name="standard" value="True"/>
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45 <param name="comprehensive" value="False"/>
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46 <param name="representation_samples" value="rows"/>
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47 <param name="matrix_attr" value="intensity"/>
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48 </conditional>
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49 <output name="hdf5_file_out" file="pm_as_bf_sf_mv.h5" ftype="h5" compare="sim_size"/>
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50 <output name="matrix_file_out" file="peak_matrix_as_bf_sf_mv.txt" ftype="tsv"/>
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51 <output name="samplelist" file="sample_list_after_mv_filter.txt" ftype="tsv"/>
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52 </test>
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53 </tests>
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54 <help>
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55 ----------------------------
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56 Missing Values Sample Filter
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57 ----------------------------
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58
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59 ..
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60
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61 ---------------------------------------------
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62
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63 Description
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64 -----------
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65
1
2cf12cd2c53a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4"
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66 Standard DIMS processing workflow: Process Scans -> [Replicate Filter] -> Align Samples -> Blank Filter -> Sample Filter -> **[Missing values sample filter]** -> Pre-processing -> Statistics
0
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67
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68 |
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69
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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.
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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71
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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.
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74 ---------------------------------------------
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75
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76 Parameters
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77 ----------
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79 **Peak Intensity Matrix (HDF5 file)** (REQUIRED) - for routine usage, the input peak intensity matrix should be that generated from the 'Align samples' tool.
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80
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81 **Maximum percentage of missing values** (REQUIRED; default = 0.8) - a numeric value ranging from 0 to 1 (decimal representation of percentage), where:
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82
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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.
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84
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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.
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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87 |
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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89 @help_options_addtional_output@
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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90
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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91 |
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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92
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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93 ---------------------------------------------
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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94
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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95 Output file(s)
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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96 --------------
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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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.
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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99
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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100
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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101 @help_outputs_matrix@
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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102
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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103 ---------------------------------------------
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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104
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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105 @github_developers_contributors@
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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106 @license@
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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107 </help>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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108 <expand macro="citations" />
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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109 </tool>
91441e41cc3d "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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110