annotate macros.xml @ 0:5e4fa4c41bde draft

"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
author computational-metabolomics
date Sat, 11 Apr 2020 16:49:37 -0400
parents
children 109c81a4138f
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5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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1 <macros>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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2 <token name="@TOOL_VERSION@">1.4.0</token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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3 <token name="@GALAXY_TOOL_VERSION@">0</token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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4
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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5 <xml name="requirements">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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6 <requirements>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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7 <requirement type="package" version="@TOOL_VERSION@">dimspy</requirement>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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8 </requirements>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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9 </xml>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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10
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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11 <token name="@HDF5_PM_TO_TXT@">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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12 dimspy hdf5-pm-to-txt
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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13 --input '$hdf5_file_out'
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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14 --output '$matrix_file_out'
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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15 --delimiter $delimiter
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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16 --attribute_name $hdf5_to_txt.matrix_attr
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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17 --representation-samples $hdf5_to_txt.representation_samples
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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18 </token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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19
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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20 <token name="@HDF5_PM_TO_TXT_COMPREHENSIVE@">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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21 dimspy hdf5-pm-to-txt
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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22 --input '$hdf5_file_out'
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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23 --output '$matrix_comprehensive_file_out'
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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24 --delimiter $delimiter
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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25 --comprehensive
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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26 --attribute_name $hdf5_to_txt.matrix_attr
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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27 --representation-samples $hdf5_to_txt.representation_samples
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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28 </token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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29
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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30 <xml name="hdf5_pm_to_txt">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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31 <section name="hdf5_to_txt" title="Show options for addtional output (*.tsv files)" expanded="False">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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32 <param name="standard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Standard output?" help="Set to &quot;yes&quot; to produce a &quot;standard&quot; Peak Matrix (i.e. m/z and intensity)."/>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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33 <param name="comprehensive" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Comprehensive output?" help="Set to &quot;yes&quot; to produce a Peak Matrix with additional information (e.g. m/z and intensity, rsd, missing values)."/>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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34 <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?" help="">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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35 <option value="rows" selected="true">Rows</option>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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36 <option value="columns">Columns</option>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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37 </param>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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38 <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values" help="">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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39 <option value="intensity" selected="true">Intensity</option>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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40 <option value="mz">m/z</option>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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41 <option value="snr">Signal-to-noise ratio (SNR)</option>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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42 </param>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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43 </section>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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44 </xml>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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45
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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46 <xml name="outputs_peak_intensity_matrix">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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47 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peak Intensity Matrix (HDF5 file)"/>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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48 <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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49 <filter>hdf5_to_txt["standard"] is True</filter>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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50 </data>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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51 <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix (comprehensive)" >
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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52 <filter>hdf5_to_txt["comprehensive"] is True</filter>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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53 </data>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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54 </xml>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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55
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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56 <xml name="citations">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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57 <citations>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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58 <citation type="doi">10.1038/nprot.2016.156</citation>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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59 <citation type="doi">10.1038/sdata.2014.12</citation>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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60 <citation type="doi">10.1021/ac062446p</citation>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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61 <citation type="doi">10.1021/ac2001803</citation>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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62 <yield />
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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63 </citations>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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64 </xml>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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65
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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66 <token name="@example_filelist@"><![CDATA[
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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67
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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68 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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69 | **filename** | **classLabel** | **replicate** | **batch** | **injectionOrder** | **[...]** |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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70 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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71 | sample_rep1.raw | sample | 1 | 1 | 1 | [...] |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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72 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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73 | sample_rep2.raw | sample | 2 | 1 | 2 | [...] |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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74 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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75 | sample_rep3.raw | sample | 3 | 1 | 3 | [...] |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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76 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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77 | sample_rep4.raw | sample | 4 | 1 | 4 | [...] |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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78 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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79 | blank_rep1.raw | blank | 1 | 1 | 5 | [...] |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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80 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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81 | blank_rep2.raw | blank | 2 | 1 | 6 | [...] |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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82 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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83 | blank_rep3.raw | blank | 3 | 1 | 7 | [...] |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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84 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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85 | blank_rep4.raw | blank | 4 | 1 | 8 | [...] |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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86 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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87 | ... | ... | ... | ... | ... | [...] |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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88 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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89
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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90 ]]></token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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91
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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92
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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93 <token name="@help_columns_peaklist@">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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94
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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95 - **mz** - the mass-to-charge ratio of the extracted mass spectral peak
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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96
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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97 - **intensity** - the intensity of the extracted mass spectral peak
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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98
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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99 - **snr** - the signal-to-noise ratio of the extracted peak, which is defined as the ratio of the peak’s intensity value to that of the background noise intensity value
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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100
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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101 - **present** - a numeric value greater than 0 that indicates the total number of scans at least one peak was detected in a given file
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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102
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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103 - **fraction** - a proportion ranging from 0 to 1 that indicates the total number of times a peak was detected in a given scan event type, divided by the total number of occurrences of that scan event type recorded in a given file.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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104
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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105 - **purity** - a numeric value ranging from 0 to 1 that indicates the proportion of scans, for a given scan event type, that contained a single mass spectral peak following hierarchical clustering. A purity score less-than 1 indicates that in some proportion of scans, multiple peaks within a single scan were grouped together during the hierarchical clustering process.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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106
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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107 - **occurrence** - a numeric value greater than 0 that indicates the total number of peaks that were observed across scans within the user-defined ppm error tolerance.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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108
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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109 - **snr_flag** - a boolean value indicating whether to keep (“1”) or discard (“0”) a peak according to its signal-to-noise ratio value.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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110
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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111 - **fraction_flag** - a boolean value indicating whether a peak should be kept or discarded according to the ratio of the number of scans in which it was detected, to the the number of scans in which it was not detected.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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112
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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113 - **flags** - a boolean value indicating whether a peak should be retained or discarded based upon both its ‘snr_flag’ and ‘fraction_flag’ boolean values (if either is set to ‘0’ i.e. discard peak, then the ‘flags’ boolean should also be 0).
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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114
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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115 </token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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116
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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117 <token name="@example_peaklist@">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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118
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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119
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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120 **Example of an processed and filtered peaklist**:
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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121
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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122
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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123 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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124 | mz | intensity | snr | present | fraction | rsd | occurrence | purity | snr_flag | fraction_flag | flags |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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125 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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126 | 90.44000 | 4744.0 | 3.06 | 1 | 0.063 | nan | 1 | 1 | 1 | 0 | 0 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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127 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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128 | 97.07380 | 5423.6 | 3.52 | 1 | 0.063 | nan | 1 | 1 | 1 | 0 | 0 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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129 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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130 | 99.04180 | 4105.8 | 3.60 | 1 | 0.063 | nan | 1 | 1 | 1 | 0 | 0 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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131 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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132 | 99.49800 | 4775.7 | 3.05 | 1 | 0.063 | nan | 1 | 1 | 1 | 0 | 0 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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133 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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134 | 99.95020 | 5657.8 | 3.63 | 1 | 0.063 | nan | 1 | 1 | 1 | 0 | 0 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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135 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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136 | 100.40660 | 5489.5 | 3.57 | 3 | 0.188 | 14.51 | 3 | 1 | 1 | 0 | 0 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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137 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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138 | 100.8672 | 4841.18 | 3.27 | 7 | 0.4375 | 16.36 | 7 | 1 | 1 | 0 | 0 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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139 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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140 | 101.0027 | 9047.79 | 5.99 | 16 | 1 | 21.53 | 19 | 0.8125 | 1 | 1 | 1 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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141 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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142 | 101.0033 | 271893.9 | 182 | 16 | 1 | 4.17 | 16 | 1 | 1 | 1 | 1 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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143 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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144 | 101.0038 | 8738.03 | 5.9 | 14 | 0.875 | 9.71 | 14 | 1 | 1 | 1 | 1 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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145 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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146 | 101.004 | 5166.67 | 3.5 | 5 | 0.3125 | 18.02 | 6 | 0.8 | 1 | 0 | 0 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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147 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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148 | 101.0599 | 5894.69 | 3.88 | 2 | 0.125 | 15.06 | 2 | 1 | 1 | 0 | 0 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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149 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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150 | 101.2728 | 6846.28 | 4.44 | 1 | 0.0625 | nan | 1 | 1 | 1 | 0 | 0 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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151 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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152
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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153 </token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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154
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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155 <token name="@help_options_addtional_output@">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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156
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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157 **Show options for additional output(s)** (OPTIONAL):
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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158
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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159 - **Standard output** (default = **No**) - boolean toggle where selection of:
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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160
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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161 - **No** - prevent the export of a .txt formatted peak matrix to the active Galaxy history.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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162
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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163 - **Yes** - export a .txt formatted peak matrix to the active Galaxy history that includes only those peaks from the input peak intensity matrix that passed the filtering procedure.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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164
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165 - **Comprehensive output** (default = "No") - boolean toggle where selection of:
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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166
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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167 - **No** - prevents export of a .txt formatted comprehensive peak matrix.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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168
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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169 - **Yes** - exports a .txt formatted comprehensive peak matrix to the active Galaxy history that contains the m/z, missing values and other metrics associated with all peaks included in the input peak intensity matrix, including the metric defined by the "The peak matrix should contain intensity | m/z | SNR values" parameter.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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170
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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171 - **Should rows or columns represent the samples?** (default = **rows**) - binary toggle where selection of:
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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172
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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173 - **rows** - sample information is presented in the rows and m/z values (for aligned mass spectral peaks) in the columns of any output peak matrix.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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174
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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175 - **columns** - sample information is presented in the columns and m/z values (for aligned mass spectral peaks) in the rows of any output peak matrix.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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176
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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177 - **The peak matrix should contain intensity | m/z | SNR values** - use this option to define which peak metric is inserted in to the cells of any optionally-output peak matrix:
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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178
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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179 - **Intensity** - writes the absolute peak intensity to the cells of the peak matrix
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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180
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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181 - **m/z** - writes the mass-to-charge ratio to the cells of the peak matrix
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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182
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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183 - **signal-to-noise ratio (SNR)** - writes the signal-to-noise ratio to the cells of the peak matrix
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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184
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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185 </token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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186
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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187 <token name="@help_outputs_matrix@">
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188
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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189 **Default output** - a HDF5 file containing the aligned peak intensity matrix.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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190
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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191 |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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192
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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193 **Optional outputs** - the metric recorded in any optionally output peak matrix/matrices is defined using the parameter "The peak matrix should contain intensity | m/z | SNR values". By default, study samples are listed row-wise, while mass-to-charge ratios of the aligned mass spectral peaks are presented in columns (to adjust, users must adjust the "Should rows or columns represent samples" toggle to “columns”).
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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194
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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195
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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196 - **Standard output** - an aligned peak matrix in tab-delimited format (“.” as decimal and NA for missing values).
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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197
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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198 **Example of a standard peak intensity matrix**:
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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199
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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200 +------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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201 | mz | 96.04216 | 99.08062 | 100.0759 | 100.8672 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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202 +------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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203 | QC_1 | 0 | 0 | 0 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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204 +------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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205 | Blank_1 | 3342.626 | 0 | 0 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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206 +------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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207 | Control_10 | 0 | 0 | 45432.2 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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208 +------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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209 | Sample_2 | 0 | 3423.3 | 0 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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210 +------------+----------+----------+----------+----------+---------+
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211 | Control_5 | 0 | 0 | 49759 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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212 +------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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213 | Control_10 | 0 | | 39890.5 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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214 +------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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215 | Sample_20 | 0 | 14563.7 | 0 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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216 +------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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217 | Sample_2 | 0 | 34676.4 | 0 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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218 +------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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219 | Sample_14 | 0 | 13134.9 | 0 | 521.4 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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220 +------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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221 | ... | ... | ... | ... | ... | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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222 +------------+----------+----------+----------+----------+---------+
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223
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224 |
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225
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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226 - **Comprehensive output** - an aligned peak matrix, as described for the "standard output" (above), including all metadata from the "Process Scans" Filelist/samplelist and the following additional mass spectral peak metrics:
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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227
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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228 - **present** - a positive integer value (0 <![CDATA[ < ]]> value <![CDATA[ < ]]> total number of study samples in the filelist / samplelist) that indicates the total number of study samples in which a peak was detected with the specified mass-to-charge ratio, plus or minus the user-defined ppm error tolerance.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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229
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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230 - **occurrence** - a positive integer value indicating the number of peaks that were grouped together during the alignment procedure and thus, that were used to calculate the average mass-to-charge ratio indicated for the aligned peak. A value greater than given in the “Present” metric indicates that one or more peaklists contained more-than one mass spectral peak with the specified mass-to-charge, plus or minus the user-defined ppm error tolerance.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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231
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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232 - **purity** - a proportion ranging from 0 to 1 that indicates the number of scans in which only a single peak was detected during the peaklist alignment process. If the value in the “occurrence” metric is greater than the “present” metric, purity will be <![CDATA[ < ]]> 1. A purity <![CDATA[ < ]]> 1 means that in at least one peaklist there was more-than one mass spectral peak with the specified mass-to-charge, plus or minus the user-defined ppm error tolerance.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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233
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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234 - **rsd_all** - a numeric value indicating the percent relative standard deviation (otherwise termed the percent coefficient of variation) of peak intensities for peaks aligned together using the Align Samples tool. If fewer than 2 peaks were aligned across samples, then the rsd_all column will be filled in with ‘nan’
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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235
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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236 - **blank_flag** (may be absent if "Blank filter” tool was not applied) - a boolean value where 0 = reject peak, 1 = accept peak. A peak is accepted during blank filtering if a user-defined minimum proportion of study samples had peak intensity values greater-than the product of the average of “reference” sample peak intensities and the “min_fold_change” parameter.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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237
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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238 - **fraction_flag** (may be absent if "Sample filter” tool was not applied)- a boolean value where 0 = reject peak, 1 = accept peak. If greater-than a user-defined minimum fraction of samples (whether checked across ALL experimental classes, or within ANY of the individual experimental classes) had recorded intensity values for a given peak, then this peak is accepted, i.e. it is considered in downstream processing procedures, while rejected peaks are not.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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239
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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240 - **flags** - a boolean value indicating whether a peak should be included (“1”) or excluded (“0”) from downstream processing procedures. Exclusion of a peak occurs if the thresholds for “relative standard deviation” and/or “minimum number of technical replicates a peak has to be present in” were not met.
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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242 |
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243
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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244 **Example of a comprehensive peak intensity matrix**:
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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245
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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246 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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247 | mz | missing values | tags_batch | tags_replicates | tags_replicate | tags_injectionOrder | tags_classLabel | tags_untyped | 96.04216 | 99.08062 | 100.0759 | 100.8672 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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248 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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249 | present* | | | | | | | | 1 | 4 | 3 | 1 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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250 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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251 | occurrence* | | | | | | | | 1 | 4 | 4 | 1 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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252 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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253 | purity* | | | | | | | | 1 | 1 | 1 | 1 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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254 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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255 | rsd_all* | | | | | | | | nan | nan | 10.98 | nan | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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256 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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257 | flags* | | | | | | | | 1 | 1 | 1 | 1 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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258 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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259 | QC_1 | 2901 | 1 | 2_3_4 | 2 | 2 | QC | | 0 | 0 | 0 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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260 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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261 | Blank_1 | 2948 | 1 | 1_2_4 | 1 | 5 | Blank | | 3342.626 | 0 | 0 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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262 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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263 | Control_10 | 2921 | 1 | 2_3_4 | 2 | 10 | Control | | 0 | 0 | 45432.2 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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264 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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265 | Sample_2 | 2819 | 1 | 1_2_4 | 1 | 13 | Exposed | | 0 | 3423.3 | 0 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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266 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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267 | Control_5 | 2877 | 1 | 2_3_4 | 2 | 18 | Control | | 0 | 0 | 49759 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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268 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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269 | Control_10 | 2856 | 1 | 1_2_3 | 1 | 21 | Control | | 0 | | 39890.5 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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270 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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271 | Sample_20 | 2855 | 1 | 1_2_4 | 1 | 25 | Exposed | | 0 | 14563.7 | 0 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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272 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
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273 | Sample_2 | 2814 | 1 | 1_2_4 | 1 | 29 | Exposed | | 0 | 34676.4 | 0 | 0 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
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274 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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275 | Sample_14 | 2870 | 1 | 1_2_3 | 1 | 33 | Exposed | | 0 | 13134.9 | 0 | 521.4 | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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276 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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277 | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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278 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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279
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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280 </token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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281
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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282
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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283 <token name="@github_developers_contributors@">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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284 Github respository (source code)
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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285 --------------------------------
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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286
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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287 Galaxy Tool Wrappers: https://github.com/computational-metabolomics/dimspy-galaxy/
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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288 DIMSpy package: https://github.com/computational-metabolomics/dimspy/
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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289
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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290
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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291 Developers and contributors
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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292 ---------------------------
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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293
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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294 - Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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295 - Martin R. Jones (m.r.jones.1@bham.ac.uk) - University of Birmingham (UK)
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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296 - Thomas Lawson (tnl495@bham.ac.uk) - University of Birmingham (UK)
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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297
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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298 </token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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299
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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300 <token name="@license@">
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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301 License
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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302 -------
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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303 DIMSpy is released under the GNU General Public License v3.0 (see `LICENSE file`_)
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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304
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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305 .. _`LICENSE file`: https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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306
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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307 </token>
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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308
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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309
5e4fa4c41bde "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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310 </macros>