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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="1.12.0">
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3 <description>Groups corresponding features from multiple maps.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</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>FeatureLinkerUnlabeled
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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 ${param_keep_subelements}
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15 -threads \${GALAXY_SLOTS:-24}
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16 -algorithm:second_nearest_gap ${param_second_nearest_gap}
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17 ${param_use_identifications}
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18 ${param_ignore_charge}
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19 -algorithm:distance_RT:max_difference ${param_max_difference}
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20 -algorithm:distance_MZ:max_difference ${param_max_difference}
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21 -algorithm:distance_MZ:unit ${param_unit}
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22 #if $adv_opts.adv_opts_selector=='advanced':
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23 -algorithm:distance_RT:exponent ${adv_opts.param_exponent}
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24 -algorithm:distance_RT:weight ${adv_opts.param_weight}
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25 -algorithm:distance_MZ:exponent ${adv_opts.param_exponent}
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26 -algorithm:distance_MZ:weight ${adv_opts.param_weight}
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27 -algorithm:distance_intensity:exponent ${adv_opts.param_exponent}
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28 -algorithm:distance_intensity:weight ${adv_opts.param_weight}
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29 #end if
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30 </command>
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31 <inputs>
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32 <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" size="20" label="input files separated by blanks" help="(-in)"/>
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33 <param name="param_keep_subelements" type="boolean" truevalue="-keep_subelements true" falsevalue="-keep_subelements false" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." help="(-keep_subelements)"/>
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34 <param name="param_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself." help="(-second_nearest_gap)"/>
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35 <param name="param_use_identifications" type="boolean" truevalue="-algorithm:use_identifications true" falsevalue="-algorithm:use_identifications false" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." help="(-use_identifications)"/>
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36 <param name="param_ignore_charge" type="boolean" truevalue="-algorithm:ignore_charge true" falsevalue="-algorithm:ignore_charge false" checked="false" optional="True" label="Compare features normally even if their charge states are different" help="(-ignore_charge)"/>
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37 <param name="param_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Maximum allowed difference in RT in seconds" help="(-max_difference)"/>
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38 <param name="param_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Maximum allowed difference in m/z (unit defined by 'unit')" help="(-max_difference)"/>
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39 <param name="param_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' parameter" help="(-unit)">
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40 <option value="Da">Da</option>
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41 <option value="ppm">ppm</option>
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42 </param>
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43 <expand macro="advanced_options">
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44 <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
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45 <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this factor" help="(-weight)"/>
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46 <param name="param_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
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47 <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="m/z distances are weighted by this factor" help="(-weight)"/>
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48 <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
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49 <param name="param_weight" type="float" min="0.0" optional="True" value="0.0" label="Distances based on relative intensity are weighted by this factor" help="(-weight)"/>
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50 </expand>
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51 </inputs>
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52 <outputs>
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53 <data name="param_out" label="Output file" format="consensusXML"/>
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54 </outputs>
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55 <help>**What it does**
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56
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57 Groups corresponding features from multiple maps.
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58
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59
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60 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerUnlabeled.html
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61
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62 @REFERENCES@
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63 </help>
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64 </tool>
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