Mercurial > repos > tomnl > mspurity_averagefragspectra

annotate averageFragSpectra.xml @ 11:36f2d807c2b8 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3
author tomnl
date Thu, 27 Jun 2019 12:32:08 -0400
parents c0b17c516c50
children e0b1da3ed06b
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1 <tool id="mspurity_averagefragspectra" name="msPurity.averageFragSpectra" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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2 <description>
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3 Average and filter LC-MS/MS fragmentation spectra (Inter, Intra or All)
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4 </description>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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10 <expand macro="requirements">
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11 </expand>
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13 <stdio>
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14 <exit_code range="1:" />
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15 </stdio>
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16 <command interpreter="Rscript"><![CDATA[
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17 averageFragSpectra.R
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18 --out_rdata="$averageFragSpectra_output_rdata"
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19 --out_peaklist="$averageFragSpectra_output_tsv"
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20 --pa="$pa"
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21 --av_level=$av_level
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22 --cores=\${GALAXY_SLOTS:-4}
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23 --minfrac=$minfrac
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24 --minnum=$minnum
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25 --ppm=$ppm
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26 --snr=$snr
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27 --ra=$ra
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28 --av=$av
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29 $sumi
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30 $rmp
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31 ]]></command>
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32 <inputs>
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33 <param name="pa" type="data" label="purityA object" format="rdata"
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34 help="purityA object saved as 'pa' in a RData file (output from frag4feature tool)"/>
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35
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36 <conditional name="av">
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37 <param name="level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
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38 <option value="intra" selected="true">within a MS data file</option>
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39 <option value="inter">accross MS data files</option>
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40 <option value="all">within and accross MS data files (ignoring intra and inter relationships)</option>
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41 </param>
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42 <when value="intra">
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43 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
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44 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
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45 </when>
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46 <when value="inter">
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47 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
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48 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
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49 </when>
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50 <when value="all">
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51 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
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52 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
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53 </when>
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54 </conditional>
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55
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56 <param name="av_level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
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57 <option value="intra" selected="true">within a MS data file</option>
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58 <option value="inter">accross MS data files</option>
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59 <option value="all">within and accross MS data files (ignoring intra and inter relationships)</option>
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60 </param>
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61 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
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62 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
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63 <param name="minfrac" type="float" min="0.0" max="1.0" value="0.5" label="Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in." help="" />
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64 <param name="minnum" type="integer" value="1" label="Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor)." help="" />
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65 <param name="ppm" type="float" value="5.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in parts per million." />
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66 <param name="sumi" type="boolean" checked="false" truevalue="--sumi" falsevalue="" label="Sum intensities across (averaged) scans?" help="" />
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67 <param name="av" type="select" label="Function to calculate the average intensity, m/z and SNR values across (averaged) scans after filtering." help="This is ignored for intensities when intensities are summed." >
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68 <option value="median" selected="true">median</option>
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69 <option value="mean">mean</option>
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70 </param>
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71
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72 <param name="rmp" type="boolean" checked="true" truevalue="--rmp" falsevalue="" label="Remove peaks that do not meet the filtering criteria. Otherwise peaks will be flagged instead."
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73 help="" />
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74 </inputs>
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75 <outputs>
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76 <data name="averageFragSpectra_output_rdata" format="rdata" label="${tool.name} (${av_level}) on ${on_string}: RData" />
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77 <data name="averageFragSpectra_output_tsv" format="tsv" label="${tool.name} (${av_level}) on ${on_string}: peaklist" />
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="av_level" value="intra" />
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82 <param name="pa" value="filterFragSpectra_output.RData" />
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83 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_intra.RData" ftype="rdata" compare="sim_size" />
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84 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_intra.tsv" ftype="tsv" />
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85 </test>
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86 <test>
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87 <param name="av_level" value="inter" />
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88 <param name="pa" value="averageFragSpectra_output_intra.RData" />
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89 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_inter.RData" ftype="rdata" compare="sim_size" />
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90 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_inter.tsv" ftype="tsv" />
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91 </test>
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92 <test>
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93 <param name="av_level" value="all" />
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94 <param name="pa" value="frag4feature_output.RData" />
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95 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_all_only.RData" ftype="rdata" compare="sim_size" />
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96 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_all_only.tsv" ftype="tsv" />
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97 </test>
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98 <test>
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99 <param name="av_level" value="all" />
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100 <param name="pa" value="averageFragSpectra_output_inter.RData" />
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101 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_all.RData" ftype="rdata" compare="sim_size" />
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102 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_all.tsv" ftype="tsv" />
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103
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104 </test>
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105 </tests>
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106
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107 <help><![CDATA[
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108 =============================================================
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109 Average Fragmentation Spectra
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110 =============================================================
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111 -----------
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112 Description
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113 -----------
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114
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115 Average and filter fragmentation spectra for each XCMS feature using an msPurity purityA object.
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116
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117 The tool uses the msPurity functions averageAllFragSpectra, averageIntraFragSpectra and
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118 averageInterFragSpectra.
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119
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120 The fragmentation spectra can be averaged in multiple ways; intra will average fragmentation
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121 spectra within an mzML file, inter will average fragmentation spectra across mzML files
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122 (requires intra to be run first) and all will average all spectra ignoring the intra and
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123 inter relationships.
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124
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125 The averaging is performed using hierarchical clustering of the m/z values of each peaks,
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126 where m/z values within a set ppm tolerance will be clustered. The clustered peaks are then
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127 averaged (or summed).
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128
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129 The fragmentation can be filtered on the averaged spectra (with the arguments snr, rsd, minfrac, ra)
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130
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131
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132 See Bioconductor documentation for more details, functions:
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133 msPurity::averageIntraFragSpectra()
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134 msPurity::averageInterFragSpectra()
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135 msPurity::averageAllFragSpectra()
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136
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137 -----------
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138 Outputs
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139 -----------
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140 * average_x_fragmentation_spectra_rdata
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141
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142 ]]></help>
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143
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144 <expand macro="citations" />
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145
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146 </tool>