Mercurial > repos > recetox > mfassignr_recallist
annotate macros.xml @ 0:6e1813883a9a draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
author | recetox |
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date | Thu, 15 Aug 2024 12:00:39 +0000 (4 months ago) |
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children | 7e5ccc8b6f6e |
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6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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1 <macros> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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2 <token name="@TOOL_VERSION@">1.0.3</token> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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3 <xml name="requirements"> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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4 <requirements> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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5 <requirement type="package" version="@TOOL_VERSION@">r-mfassignr</requirement> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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6 </requirements> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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7 </xml> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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8 |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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9 <xml name="refs"> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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10 <xrefs> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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11 <xref type="bio.tools">mfassignr</xref> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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12 </xrefs> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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13 </xml> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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14 |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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15 <xml name="creator"> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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16 <creator> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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17 <person |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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18 givenName="Kristina" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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19 familyName="Gomoryova" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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20 url="https://github.com/KristinaGomoryova" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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21 identifier="0000-0003-4407-3917" /> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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22 <person |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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23 givenName="Helge" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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24 familyName="Hecht" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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25 url="https://github.com/hechth" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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26 identifier="0000-0001-6744-996X" /> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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27 <person |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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28 givenName="Zargham" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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29 familyName="Ahmad" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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30 url="https://github.com/zargham-ahmad" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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31 identifier="0000-0002-6096-224X" /> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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32 <organization |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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33 url="https://www.recetox.muni.cz/" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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34 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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35 name="RECETOX MUNI" /> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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36 </creator> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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37 </xml> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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38 |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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39 <xml name="kmdnoise_param"> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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40 <param name="input_file" type="data" format="tabular" label="Input data" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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41 help= "Input data frame, first column is mass, second column is intensity"/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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42 <param name="upper_y" type="float" label="upper limit for the y intercept" value="0.2" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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43 help= "The upper y-intercept value to isolate noise peaks in the equation for the KMD plot: y = 0.001123*x + b. Default value is set to 0.2, so that it does not interact with any potentially double-charged peaks."/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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44 <param name="lower_y" type="float" label="lower limit for the y intercept" value="0.05" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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45 help="The lower y-intercept value to isolate noise peaks in the equation for the KMD plot: y = 0.001123*x + b. Default value is set to 0.05 to ensure no analyte peaks are incorporated into the noise estimation."/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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46 <param name="upper_x" optional="true" type="float" label="upper limit for the x intercept" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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47 help="If not set, it defaults to maximum mass in the mass spectrum."/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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48 <param name="lower_x" optional="true" type="float" label="lower limit for the x intercept" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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49 help="If not set, it defaults to minimum mass in the mass spectrum."/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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50 </xml> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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51 |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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52 <xml name="histnoise_param"> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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53 <param name="input_file" type="data" format="tabular" label="Input data" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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54 help= "Input data frame, first column is mass, second column is intensity"/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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55 <param name="SN" type="float" label="signal-to-noise threshold" value="0" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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56 help= "A numeric value for situations where a predefined noise value is desired, default is 0"/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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57 <param name="bin" type="float" label="bindwidth of the histogram" value="0.01" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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58 help= "A numeric value determining the binwidth of the histogram, default is 0.01"/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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59 </xml> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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60 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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61 <xml name="noise_threshold_params"> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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62 <param name="sn_ratio" type="float" label="SN ratio" value="6" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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63 help= "Noise multiplier. Recommended value is 6."/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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64 <param name="kmdn" type="float" label="Estimated noise" value="0" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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65 help= "Estimated noise, either from the KMDNoise or HistNoise function."/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
recetox
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66 </xml> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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67 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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68 <xml name="snplot_param"> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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69 <param name="input_file" type="data" format="tabular" label="Input data" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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70 help= "Input data frame, first column is mass, second column is intensity"/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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71 <param name="cut" type="float" label="cut" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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72 help= "A numeric value of the intensity cut value being investigated"/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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73 <param name="mass" type="float" label="mass" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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74 help= "A numeric value setting a centerpoint to look at the mass spectrum"/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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75 <param name="window_x" type="float" label="window.x" value="0.5" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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76 help= "A numeric value setting the +/- range around the mass centerpoint, default is 0.5"/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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77 <param name="window_y" type="float" label="window.y" value="10" |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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78 help= "A numeric value setting the y axis value for the plot, determined by multiplying the cut by this value"/> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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79 </xml> |
6e1813883a9a
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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80 |
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81 <xml name="ionmode_param"> |
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82 <param name="ionmode" type="select" display="radio" label="Ion mode" help= "The ionization mode."> |
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83 <option value="neg" >negative</option> |
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84 <option value="pos" selected="true">positive</option> |
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85 </param> |
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86 </xml> |
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87 |
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88 <xml name="mfassign_param"> |
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89 <param name="ppm_err" type="integer" label="ppm_err" |
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90 help= "Error tolerance (ppm) for formula assignment" value="3"/> |
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91 <expand macro="ionmode_param" /> |
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92 <expand macro="noise_threshold_params" /> |
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93 <param name="lowMW" type="float" label="Lower limit of molecular mass to be assigned" value="100" |
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94 help= "Lower limit of molecular mass to be assigned."/> |
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95 <param name="highMW" type="float" label="Upper limit of molecular mass to be assigned" value="1000" |
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96 help= "Upper limit of molecular mass to be assigned."/> |
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97 </xml> |
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98 |
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99 <xml name="recal_param"> |
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100 <param name="input_file" type="data" format="tabular" label="Input data (Output from MFAssign)" |
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101 help= "Input data frame, the output from MFAssign or MFAssignCHO"/> |
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102 <param name="series" type="data" format="tabular" label="Calibration series (Output from RecalList)" |
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103 help= "Calibration series (Output from RecalList). At maximum the first 10 rows are used."/> |
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104 <param name="peaks" type="data" format="tabular" label="Peaks dataframe (Mono from IsoFiltR)" |
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105 help= "Peaks data frame, the Mono output from IsoFiltR"/> |
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106 <param name="isopeaks" type="data" format="tabular" label="Isopeaks dataframe (Iso from IsoFiltR)" |
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107 optional="true" help= "Isopeaks data frame, the Mono output from IsoFiltR"/> |
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108 <expand macro="ionmode_param" /> |
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109 <expand macro="noise_threshold_params" /> |
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110 <param name="mzRange" type="float" label="Mass windows used for the segmented recalibration" value="30" |
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111 help= "Mass windows used for the segmented recalibration"/> |
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112 <param name="step_O" type="float" label="Number of oxygen steps for formula extension" value="3" |
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113 help= "Number of oxygen steps for formula extension"/> |
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114 <param name="step_H2" type="float" label="Number of H2 steps for formula extension" value="5" |
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115 help= "Number of H2 steps for formula extension"/> |
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116 <param name="CalPeak" type="float" label="Maximum allowed recalibrant peaks per mzRange defined segment" value="150" help= "Maximum allowed recalibrant peaks per mzRange defined segment"/> |
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117 |
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118 </xml> |
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119 |
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120 <xml name="isofiltr_param"> |
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121 <param name="peaks" type="data" format="tabular" label="Input Peak Data" |
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122 help="The input data frame containing abundance and peak mass."/> |
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123 <param name="SN" type="float" value="0" label="Signal-to-Noise Ratio" |
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124 help="Sets the noise cut for the data; peaks below this value will not be evaluated."/> |
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125 <param name="Carbrat" type="float" value="60" min="5" label="Maximum 13C/12C Ratio" |
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126 help="Sets the maximum allowed ratio for matching 13C isotopes."/> |
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127 <param name="Sulfrat" type="float" value="30" label="Maximum 34S/32S Ratio" |
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128 help="Sets the maximum allowed ratio for matching 34S isotopes."/> |
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129 <param name="Sulferr" type="float" value="5" label="Maximum Error for 34S Matching (ppm)" |
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130 help="Sets the maximum allowed error (ppm) for 34S mass matching."/> |
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131 <param name="Carberr" type="float" value="5" label="Maximum Error for 13C Matching (ppm)" |
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132 help="Sets the maximum allowed error (ppm) for 13C mass matching."/> |
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133 </xml> |
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134 |
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135 <xml name="citations"> |
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136 <citations> |
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137 <citation type="doi">10.1016/j.envres.2020.110114</citation> |
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138 </citations> |
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139 </xml> |
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140 |
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141 </macros> |