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1 <tool id="flashlfq" name="FlashLFQ" version="0.1.0">
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2 <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
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3 <requirements>
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4 <requirement type="package" version="0.199.0">flashlfq</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 FlashLFQ --idt $idt --rep Test2 --ppm $psm --iso $iso
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8 #if $intensity == 'integrate':
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9 --int true
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10 #end if
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11 #if $charge == 'precursor':
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12 --chg true
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13 #end if
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14 --pau false
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15 ]]></command>
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16 <inputs>
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17 <param name="idt" type="data" format="tabular" label="identification file"/>
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18 <param name="scans" type="data" format="mzml" multiple="true" label="spectrum files"/>
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19 <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>
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20 <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>
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21 <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/>
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22 <param name="intensity" type="select" label="intensity">
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23 <option value="apex" selected="true">use the apex intensity</option>
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24 <option value="integrate">integrate chromatographic peak intensity</option>
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25 </param>
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26 <param name="charge" type="select" label="charge">
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27 <option value="all" selected="true">use all identification detected charge states</option>
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28 <option value="precursor">use precursor charge</option>
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29 </param>
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30 <!--
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31 -->
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32 </inputs>
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33 <outputs>
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34 <data name="log" format="text" label="${tool.name} on ${on_string}: Log" />
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35 <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv" />
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36 <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv" />
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37 <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" />
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38 <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="idt" value="aggregatePSMs_5ppmAroundZero.psmtsv" ftype="tabular"/>
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43 <param name="scans" value="sliced-mzml.mzML" ftype="mzml"/>
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44 <param name="ppm" value="12"/>
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45 <param name="iso" value="6"/>
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46 <output name="log">
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47 <assert_contents>
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48 <has_text text="ppmTolerance = 10" />
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49 <has_text text="isotopePpmTolerance = 6" />
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50 </assert_contents>
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51 </output>
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55
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56
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57
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58 **Accepted command-line arguments:**
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59
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60 --idt [string | identification file path (TSV format)]
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61
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62 --raw [string | MS data file (.raw or .mzML)]
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63
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64 --rep [string | repository containing MS data files]
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65
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66 --ppm [double | monoisotopic ppm tolerance] (default = 10)
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67
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68 --iso [double | isotopic distribution tolerance in ppm] (default = 5)
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69
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70 --sil [boolean | silent mode; no console output] (default = false)
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71
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72 --pau [boolean | pause at end of run] (default = true)
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73
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74 --int [boolean | integrate chromatographic peak intensity instead of using
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75 the apex intensity] (default = false)
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76
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77 --chg [boolean | use only precursor charge state; when set to false, FlashLFQ looks
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78 for all charge states detected in the MS/MS identification file for each peptide] (default = false)
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79
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80 --mbr [bool|match between runs]
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81
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82 --rmm [bool|require observed monoisotopic mass peak]
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83
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84 --nis [int|number of isotopes required to be observed]
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85
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86
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87 ]]></help>
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88 <citations>
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89 <citation type="doi">10.1021/acs.jproteome.7b00608</citation>
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90 </citations>
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91 </tool>
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