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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="0.1.99">flashlfq</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 #import re
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8 #set $idt_path = $re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1]) + ".psmtsv"
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9 ## cp '${idt}' '${idt_path}';
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10 ln -s '${idt}' '${idt_path}';
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11 #for $peak_list in $peak_lists:
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12 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML"
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13 ln -s '${peak_list}' '${input_name}';
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14 #end for
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15 FlashLFQ --idt $idt_path --rep `pwd` --ppm $ppm --iso $iso --nis $nis
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16 #if $intensity == 'integrate':
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17 --int true
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18 #end if
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19 #if $charge == 'precursor':
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20 --chg true
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21 #end if
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22 $rmm $mbr
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23 --pau false
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24 && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log'
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25 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences'
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26 && cp *_FlashLFQ_QuantifiedModifiedSequences.tsv '$quantifiedModifiedSequences'
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27 && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks'
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28 && cp *_FlashLFQ_QuantifiedProteins.tsv '$quantifiedProteins'
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29 ]]></command>
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30 <inputs>
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31 <param name="idt" type="data" format="tabular" label="identification file"/>
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32 <param name="peak_lists" type="data" format="mzml" multiple="true" label="spectrum files"/>
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33 <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>
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34 <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>
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35 <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/>
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36 <param name="intensity" type="select" label="intensity">
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37 <option value="apex" selected="true">use the apex intensity</option>
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38 <option value="integrate">integrate chromatographic peak intensity</option>
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39 </param>
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40 <param name="charge" type="select" label="charge">
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41 <option value="all" selected="true">use all identification detected charge states</option>
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42 <option value="precursor">use precursor charge</option>
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43 </param>
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44 <param name="rmm" type="boolean" truevalue="--rmm true" falsevalue="--rmm false" checked="true"
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45 label="require observed monoisotopic mass peak"/>
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46 <param name="mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false"
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47 label="match between runs"/>
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48 </inputs>
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49 <outputs>
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50 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" />
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51 <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv" />
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52 <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv" />
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53 <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" />
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54 <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" />
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="idt" value="aggregatePSMs_5ppmAroundZero.psmtsv" ftype="tabular"/>
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59 <param name="scans" value="sliced-mzml.mzML" ftype="mzml"/>
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60 <param name="ppm" value="12"/>
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61 <param name="iso" value="6"/>
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62 <output name="log">
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63 <assert_contents>
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64 <has_text text="ppmTolerance = 12" />
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65 <has_text text="isotopePpmTolerance = 6" />
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66 </assert_contents>
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67 </output>
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71
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72 **FlashLFQ**
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73
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74 **Accepted command-line arguments:**
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75
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76 ::
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77
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78 --idt [string | identification file path (TSV format)]
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79 --raw [string | MS data file (.raw or .mzML)]
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80 --rep [string | repository containing MS data files]
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81 --ppm [double | monoisotopic ppm tolerance] (default = 10)
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82 --iso [double | isotopic distribution tolerance in ppm] (default = 5)
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83 --sil [boolean | silent mode; no console output] (default = false)
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84 --pau [boolean | pause at end of run] (default = true)
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85 --int [boolean | integrate chromatographic peak intensity instead of using
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86 the apex intensity] (default = false)
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87 --chg [boolean | use only precursor charge state; when set to false, FlashLFQ looks
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88 for all charge states detected in the MS/MS identification file for each peptide] (default = false)
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89 --mbr [bool|match between runs]
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90 --rmm [bool|require observed monoisotopic mass peak]
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91 --nis [int|number of isotopes required to be observed]
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92
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93
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94 ]]></help>
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95 <citations>
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96 <citation type="doi">10.1021/acs.jproteome.7b00608</citation>
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97 </citations>
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98 </tool>
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