Mercurial > repos > computational-metabolomics > dimspy_align_samples

annotate align_samples.xml @ 0:33b65dacd377 draft

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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
author computational-metabolomics
date Sat, 11 Apr 2020 16:51:19 -0400
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children c72868b80c29
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33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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1 <tool id="dimspy_align_samples" name="Align Samples" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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2 <description> - Align peaks across Peaklists</description>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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3 <macros>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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4 <import>macros.xml</import>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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5 </macros>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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6 <expand macro="requirements" />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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7 <command detect_errors="exit_code">
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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8 <![CDATA[
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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9 dimspy align-samples
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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10 --input '$hdf5_file_in'
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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11 --output '$hdf5_file_out'
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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12 #if $filelist
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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13 --filelist '$filelist'
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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14 #end if
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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15 --ppm $ppm
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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16 #if $hdf5_to_txt.standard
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17 &&
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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18 @HDF5_PM_TO_TXT@
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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19 #end if
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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20 #if $hdf5_to_txt.comprehensive
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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21 &&
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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22 @HDF5_PM_TO_TXT_COMPREHENSIVE@
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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23 #end if
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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24 ]]>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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25 </command>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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26 <inputs>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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27 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peaklists (HDF5 file)" help="" />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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28 <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" optional="true" label="Filelist / Samplelist" help="Only provide a filelist if you like to exclude Peaklists, update the metadata (e.g. classLabel), or if you have not provided a filelist for Process Scans or Replicate Filter." />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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29 <param name="ppm" argument="--ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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30 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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31 <expand macro="hdf5_pm_to_txt" />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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32 </inputs>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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33 <outputs>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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34 <expand macro="outputs_peak_intensity_matrix" />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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35 </outputs>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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36 <tests>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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37 <test>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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38 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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39 <param name="ppm" value="2.0"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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40 <param name="delimiter" value="tab"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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41 <conditional name="hdf5_to_txt" >
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42 <param name="standard" value="True"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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43 <param name="comprehensive" value="False"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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44 <param name="samples_representations" value="rows"/>
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45 <param name="matrix_attr" value="intensity"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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46 </conditional>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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47 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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48 <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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49 </test>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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50 <test>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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51 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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52 <param name="ppm" value="2.0"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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53 <param name="delimiter" value="tab"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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54 <conditional name="hdf5_to_txt">
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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55 <param name="standard" value="True"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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56 <param name="comprehensive" value="False"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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57 <param name="representation_samples" value="columns"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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58 <param name="matrix_attr" value="intensity"/>
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59 </conditional>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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60 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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61 <output name="matrix_file_out" file="peak_matrix_as_t.txt" ftype="tsv"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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62 </test>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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63 <test>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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64 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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65 <param name="ppm" value="2.0"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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66 <param name="delimiter" value="tab"/>
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67 <conditional name="hdf5_to_txt">
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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68 <param name="standard" value="True"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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69 <param name="comprehensive" value="True"/>
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70 <param name="samples_representations" value="rows"/>
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71 <param name="matrix_attr" value="mz"/>
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72 </conditional>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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73 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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74 <output name="matrix_file_out" file="peak_matrix_as_mz.txt" ftype="tsv"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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75 <output name="matrix_comprehensive_file_out" file="peak_matrix_as_mz_compr.txt" ftype="tsv"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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76 </test>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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77 </tests>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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78 <help>
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79 -------------
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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80 Align Samples
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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81 -------------
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82
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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83 ..
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84
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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85 -------------------------------
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86
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87 Description
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88 -----------
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89
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90 Standard DIMS processing workflow: Process Scans -> Replicate Filter -> **Align Samples** -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics
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92 |
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94 This tool takes the peaklists for all study samples and merges them in to single aligned peak matrix. The peak matrix comprises a table, with samples along one axis and the mass-to-charge ratios of detected mass spectral peaks along the opposite axis. At the intersection of sample and mass-to-charge ratio, the intensity is given for a specific peak in a specific sample (if no intensity recorded, then ‘0’ is inserted).
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96 -------------------------------
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97
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98 Parameters
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99 ----------
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101 **Peaklists (HDF5 file)** (REQUIRED) - a HDF5 file containing all peaklists to undergo alignment.
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103 |
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104
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105 **Filelist / Samplelist** (REQUIRED) - a file of type ‘tabular’ with the following required columns (additional metadata columns may also be included, e.g. “collectionTime”, etc.):
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106
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107 - **filename** - the name of the .raw or .mzML files from which peaklists were extracted using the “Process Scans” tool
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108
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109 - **batch** - a numeric value indicating the analysis batches samples were analysed in (if a single large analytica run then the default = 1)
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110
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111 - **classLabel** - a string indicating the experiment classes the samples belong to (e.g. control, QC, blank/placebo, exposed/treatment)
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112
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113 - **injectionOrder** - a numeric value indicating the order in which samples were analysed.
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115 |
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116
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117 **ppm error tolerance** (REQUIRED; default = 2.0) - a numeric value equal-to or greater-than 0.
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118
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119 This parameter will influence the alignment of peaks from input peaklists. Peaks from distinct peaklists (corresponding to individual study samples) are aligned if the difference between their mass-to-charge ratios, when divided by the average of their mass-to-charge ratios and multiplied by 1 × 10\ :sup:`6` \, is equal-to or less-than than this parameter value (i.e. the difference between the mass-to-charge ratios, measured on the ppm scale, is less than the user-defined “ppm error tolerance”).
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120
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121 |
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122
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123 @help_options_addtional_output@
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125 |
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126
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127 ------------------------------
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128
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129 Output file(s)
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130 --------------
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132 @help_outputs_matrix@
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133
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134 -------------------------------------------------------------
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135
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136 @github_developers_contributors@
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137 @license@
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138 </help>
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139 <expand macro="citations" />
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140 </tool>