Mercurial > repos > computational-metabolomics > dimspy_missing_values_sample_filter
annotate missing_values_sample_filter.xml @ 1:2cf12cd2c53a draft
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4"
author | computational-metabolomics |
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date | Tue, 28 Apr 2020 17:27:23 -0400 |
parents | 91441e41cc3d |
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rev | line source |
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91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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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"
computational-metabolomics
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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"
computational-metabolomics
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3 <macros> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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4 <import>macros.xml</import> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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5 </macros> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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6 <expand macro="requirements" /> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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7 <command detect_errors="exit_code"> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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8 <![CDATA[ |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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9 dimspy mv-sample-filter |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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10 --input '$hdf5_file_in' |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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11 --output '$hdf5_file_out' |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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12 --max-fraction $max_fraction |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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13 && |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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14 dimspy create-sample-list |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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15 --input '$hdf5_file_out' |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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16 --output '$samplelist' |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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17 --delimiter tab |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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18 #if $hdf5_to_txt.standard |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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19 && |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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20 @HDF5_PM_TO_TXT@ |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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21 #end if |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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22 #if $hdf5_to_txt.comprehensive |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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23 && |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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24 @HDF5_PM_TO_TXT_COMPREHENSIVE@ |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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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"
computational-metabolomics
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27 </command> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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28 <inputs> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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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"
computational-metabolomics
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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> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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35 <expand macro="outputs_peak_intensity_matrix" /> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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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"/> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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42 <param name="delimiter" value="tab"/> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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43 <conditional name="hdf5_to_txt"> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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44 <param name="standard" value="True"/> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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45 <param name="comprehensive" value="False"/> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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46 <param name="representation_samples" value="rows"/> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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47 <param name="matrix_attr" value="intensity"/> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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48 </conditional> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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49 <output name="hdf5_file_out" file="pm_as_bf_sf_mv.h5" ftype="h5" compare="sim_size"/> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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50 <output name="matrix_file_out" file="peak_matrix_as_bf_sf_mv.txt" ftype="tsv"/> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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51 <output name="samplelist" file="sample_list_after_mv_filter.txt" ftype="tsv"/> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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52 </test> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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53 </tests> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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54 <help> |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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55 ---------------------------- |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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56 Missing Values Sample Filter |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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57 ---------------------------- |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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58 |
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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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59 .. |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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60 |
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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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61 --------------------------------------------- |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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62 |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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63 Description |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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64 ----------- |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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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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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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67 |
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68 | |
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69 |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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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. |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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73 |
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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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74 --------------------------------------------- |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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75 |
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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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76 Parameters |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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77 ---------- |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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78 |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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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. |
91441e41cc3d
"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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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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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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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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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. |
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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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86 |
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87 | |
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88 |
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89 @help_options_addtional_output@ |
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90 |
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91 | |
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93 --------------------------------------------- |
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94 |
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95 Output file(s) |
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96 -------------- |
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97 |
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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. |
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99 |
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101 @help_outputs_matrix@ |
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102 |
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103 --------------------------------------------- |
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104 |
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105 @github_developers_contributors@ |
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106 @license@ |
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107 </help> |
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108 <expand macro="citations" /> |
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109 </tool> |
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110 |