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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="SpectraMerger" name="SpectraMerger" version="1.12.0">
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3 <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">SpectraMerger</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>SpectraMerger
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -merging_method ${param_merging_method}
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15 -threads \${GALAXY_SLOTS:-24}
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16 -algorithm:block_method:ms_levels ${param_ms_levels}
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17 -algorithm:block_method:rt_block_size ${param_rt_block_size}
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18 -algorithm:block_method:rt_max_length ${param_rt_max_length}
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19 -algorithm:precursor_method:mz_tolerance ${param_mz_tolerance}
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20 -algorithm:precursor_method:rt_tolerance ${param_rt_tolerance}
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21 #if $adv_opts.adv_opts_selector=='advanced':
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22 -algorithm:mz_binning_width ${adv_opts.param_mz_binning_width}
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23 -algorithm:mz_binning_width_unit ${adv_opts.param_mz_binning_width_unit}
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24 -algorithm:sort_blocks ${adv_opts.param_sort_blocks}
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25 #end if
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26 </command>
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27 <inputs>
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28 <param name="param_in" type="data" format="mzML" optional="False" label="Input mzML file." help="(-in)"/>
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29 <param name="param_merging_method" type="select" optional="True" value="block_method" label="Method of merging which should be used." help="(-merging_method)">
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30 <option value="precursor_method">precursor_method</option>
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31 <option value="block_method">block_method</option>
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32 </param>
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33 <param name="param_ms_levels" type="text" min="1" optional="True" size="20" value="1" label="Merge spectra of this level. All spectra with other MS levels remain untouched." help="(-ms_levels)"/>
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34 <param name="param_rt_block_size" type="integer" min="1" optional="True" value="5" label="Maximum number of scans to be summed up." help="(-rt_block_size)"/>
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35 <param name="param_rt_max_length" type="float" min="0.0" max="1e+11" optional="True" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)." help="(-rt_max_length)"/>
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36 <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]." help="(-mz_tolerance)"/>
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37 <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]." help="(-rt_tolerance)"/>
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38 <expand macro="advanced_options">
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39 <param name="param_mz_binning_width" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of two peaks to be merged." help="(-mz_binning_width)"/>
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40 <param name="param_mz_binning_width_unit" type="select" optional="True" value="Da" label="Unit in which the distance between two peaks is given." help="(-mz_binning_width_unit)">
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41 <option value="Da">Da</option>
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42 <option value="ppm">ppm</option>
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43 </param>
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44 <param name="param_sort_blocks" type="select" optional="True" value="RT_ascending" label="Sort blocks by <?> before merging them (useful for precursor order)" help="(-sort_blocks)">
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45 <option value="RT_ascending">RT_ascending</option>
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46 <option value=" RT_descending"> RT_descending</option>
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47 </param>
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48 </expand>
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49 </inputs>
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50 <outputs>
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51 <data name="param_out" label="Output mzML file with merged spectra." format="mzML"/>
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52 </outputs>
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53 <help>**What it does**
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54
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55 Merges spectra (each MS level separately), increasing S/N ratios.
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56
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57
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58 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html
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59
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60 @REFERENCES@
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61 </help>
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62 </tool>
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