Mercurial > repos > tomnl > create_sqlite_db
annotate macros.xml @ 28:be54f396ecfe draft default tip
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
author | tomnl |
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date | Wed, 18 Jul 2018 05:47:49 -0400 |
parents | 0d59d313d3f8 |
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rev | line source |
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fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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1 <?xml version="1.0"?> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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2 <macros> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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3 <xml name="requirements"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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4 <requirements> |
27
0d59d313d3f8
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
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5 <requirement type="package" version="1.7.7" >bioconductor-mspurity</requirement> |
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fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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6 <yield /> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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7 </requirements> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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8 |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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9 </xml> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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10 |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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11 <xml name="offsets"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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12 <param name="minoffset" type="float" label="minoffset" value="0.5" |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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13 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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14 100.0 then the range would be from 999.5 to 100.0"/> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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15 <param name="maxoffset" type="float" label="maxoffset" value="0.5" |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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16 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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17 100.0 then the range would be from 100.0 to 100.5"/> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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18 </xml> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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19 <xml name="general_params"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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20 |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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21 <param name="ilim" type="float" label="ilim" value="0.05" |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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22 help="All peaks less than this percentage of the target peak will be removed |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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23 from the purity calculation, default is 5\% (0.05)"/> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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24 |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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25 <param name="iw_norm" type="select" label="Normalisation for isolation efficiency"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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26 <option value="gauss" >Gaussian</option> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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27 <option value="rcosine" >Raised cosine</option> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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28 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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29 <option value="none" selected="true" >No normalisation</option> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
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30 </param> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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31 |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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32 <conditional name="isotopes"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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33 <param name="isotopes" type="select" label="Handling of isotopic peaks" > |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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34 <option value="keep" >Keep isotopes in precursor ion purity calculation</option> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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35 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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36 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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37 </param> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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38 <when value="keep"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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39 </when> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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40 <when value="exclude_default"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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41 </when> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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42 <when value="user"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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43 <param name="im" type="data" format="tabular" label="Isotope matrix" help=" |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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44 tabular file composing of columns: |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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45 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer', |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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46 'charge', 'relative atomic mass (int)', 'xflag']. |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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47 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant. |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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48 e.g. for c12 to c13, the c13 is less abundant so we flag as 1 for Li6 to Li7, the Li7 is more abundant |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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49 so we would flag as 0. |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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50 Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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51 </when> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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52 </conditional> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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53 </xml> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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54 |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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55 |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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56 <xml name="camera_xcms"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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57 <param name="camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?" |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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58 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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59 xa (or both). The XCMS object is nested within the CAMERA object so either can be used"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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60 <option value="xcms" selected="true" >XCMS (xset)</option> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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61 <option value="camera" >CAMERA (xa)</option> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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62 </param> |
fe7d7cc95ca5
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63 </xml> |
fe7d7cc95ca5
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64 |
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65 |
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66 <xml name="fileload"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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67 <conditional name="file_load_conditional"> |
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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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68 <param name="file_load_select" type="select" label="Resubmit your dataset" |
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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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69 help="Use only if you get a message which say that your original dataset or |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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70 dataset collection can not be found the server." > |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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71 <option value="no" >no need</option> |
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72 <option value="yes" >yes</option> |
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73 </param> |
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74 <when value="no"> |
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75 </when> |
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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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76 <when value="yes"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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77 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf" |
fe7d7cc95ca5
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78 multiple="true" label="File(s) from your history containing your chromatograms" |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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79 help="Select the dataset collection containing the files that were used |
fe7d7cc95ca5
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80 for processing" /> |
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81 </when> |
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82 </conditional> |
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83 </xml> |
fe7d7cc95ca5
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84 |
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85 <xml name="grp_peaklist"> |
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86 <conditional name="grp_peaklist_opt"> |
fe7d7cc95ca5
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
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87 <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?"> |
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88 <option value="yes" >Provide group peaklist </option> |
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89 <option value="no" selected="true">Use default grouped peaklist</option> |
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90 </param> |
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91 <when value="no"> |
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92 </when> |
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93 <when value="yes"> |
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94 <param type="data" name="grp_peaklist" label="grouped peaklist" |
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95 help="User supplied grouped peaklist to add to the database (if additional columns required e.g. |
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96 CAMERA annotations" format="tsv,tabular"/> |
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97 </when> |
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98 </conditional> |
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99 </xml> |
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100 |
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101 <xml name="citations"> |
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102 <citations> |
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103 <citation type="doi">10.1021/acs.analchem.6b04358</citation> |
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104 <yield /> |
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105 </citations> |
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106 </xml> |
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107 |
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108 </macros> |