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annotate macros.xml @ 3:2766f2a85997 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
author tomnl
date Fri, 30 Mar 2018 10:12:19 -0400
parents fe7d7cc95ca5
children bc86834acaed
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="1.5.4" >bioconductor-mspurity</requirement>
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6 <requirement type="package" version="1.4.4" >r-optparse</requirement>
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7 <yield />
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8 </requirements>
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10 </xml>
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12 <xml name="offsets">
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13 <param name="minoffset" type="float" label="minoffset" value="0.5"
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14 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
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15 100.0 then the range would be from 999.5 to 100.0"/>
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16 <param name="maxoffset" type="float" label="maxoffset" value="0.5"
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17 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is
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18 100.0 then the range would be from 100.0 to 100.5"/>
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19 </xml>
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20 <xml name="general_params">
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22 <param name="ilim" type="float" label="ilim" value="0.05"
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23 help="All peaks less than this percentage of the target peak will be removed
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24 from the purity calculation, default is 5\% (0.05)"/>
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25
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26 <param name="iw_norm" type="select" label="Normalisation for isolation efficiency">
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27 <option value="gauss" >Gaussian</option>
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28 <option value="rcosine" >Raised cosine</option>
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29 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
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30 <option value="none" selected="true" >No normalisation</option>
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31 </param>
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33 <conditional name="isotopes">
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34 <param name="isotopes" type="select" label="Handling of isotopic peaks" >
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35 <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
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36 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
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37 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
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38 </param>
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39 <when value="keep">
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40 </when>
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41 <when value="exclude_default">
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42 </when>
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43 <when value="user">
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44 <param name="im" type="data" format="tabular" label="Isotope matrix" help="
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45 tabular file composing of columns:
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46 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
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47 'charge', 'relative atomic mass (int)', 'xflag'].
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48 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
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49 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
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50 so we would flag as 0.
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51 Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>
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52 </when>
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53 </conditional>
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54 </xml>
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55
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56
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57 <xml name="camera_xcms">
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58 <param name="camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?"
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59 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called
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60 xa (or both). The XCMS object is nested within the CAMERA object so either can be used">
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61 <option value="xcms" selected="true" >XCMS (xset)</option>
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62 <option value="camera" >CAMERA (xa)</option>
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63 </param>
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64 </xml>
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65
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66
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67 <xml name="fileload">
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68 <conditional name="file_load_conditional">
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69 <param name="file_load_select" type="select" label="Resubmit your dataset"
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70 help="Use only if you get a message which say that your original dataset or
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71 dataset collection can not be found the server." >
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72 <option value="no" >no need</option>
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73 <option value="yes" >yes</option>
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74 </param>
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75 <when value="no">
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76 </when>
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77 <when value="yes">
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78 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf"
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79 multiple="true" label="File(s) from your history containing your chromatograms"
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80 help="Select the dataset collection containing the files that were used
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81 for processing" />
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82 </when>
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83 </conditional>
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84 </xml>
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85
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86 <xml name="grp_peaklist">
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87 <conditional name="grp_peaklist_opt">
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88 <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
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89 <option value="yes" >Provide group peaklist </option>
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90 <option value="no" selected="true">Use default grouped peaklist</option>
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91 </param>
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92 <when value="no">
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93 </when>
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94 <when value="yes">
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95 <param type="data" name="grp_peaklist" label="grouped peaklist"
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96 help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
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97 CAMERA annotations" format="tsv,tabular"/>
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98 </when>
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99 </conditional>
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100 </xml>
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101
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102 <xml name="citations">
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103 <citations>
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104 <citation type="doi">10.1021/acs.analchem.6b04358</citation>
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105 <yield />
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106 </citations>
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107 </xml>
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108
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109 </macros>