Mercurial > repos > galaxyp > flashlfq
annotate flashlfq.xml @ 9:944d155c01c9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
| author | galaxyp |
|---|---|
| date | Wed, 30 Jan 2019 05:38:43 -0500 |
| parents | 69cd4ab3145b |
| children | a21452a5c952 |
| rev | line source |
|---|---|
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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changeset
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1 <tool id="flashlfq" name="FlashLFQ" version="0.1.111"> |
| 0 | 2 <description>ultrafast label-free quantification for mass-spectrometry proteomics</description> |
| 3 <requirements> | |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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4 <requirement type="package" version="0.1.111">flashlfq</requirement> |
| 0 | 5 </requirements> |
| 6 <command><![CDATA[ | |
| 2 | 7 #import re |
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41c0c75301b3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty
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8 #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv" |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
galaxyp
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9 ln -s '${idt}' '${idt_path}' && |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
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10 mkdir spectrum_dir && |
| 2 | 11 #for $peak_list in $peak_lists: |
| 12 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML" | |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
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13 ln -s '${peak_list}' 'spectrum_dir/${input_name}' && |
| 2 | 14 #end for |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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changeset
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15 #if $normalize.nor == 'true': |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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16 #set $input_name = $re.sub('[.][^.]*$','',$experimental_design.display_name.split('/')[-1]) + ".tsv" |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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17 ln -s '${experimental_design}' 'spectrum_dir/${input_name}' && |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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18 #end if |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
galaxyp
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changeset
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19 FlashLFQ |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
galaxyp
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20 --idt '$idt_path' |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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21 --rep "./spectrum_dir" |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
galaxyp
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changeset
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22 --ppm $ppm |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
galaxyp
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changeset
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23 --iso $iso |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
galaxyp
parents:
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changeset
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24 --nis $nis |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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changeset
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25 #if $normalize.nor == 'true': |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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changeset
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26 --nor true |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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changeset
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27 #end if |
| 0 | 28 #if $intensity == 'integrate': |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
galaxyp
parents:
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changeset
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29 --int true |
| 0 | 30 #end if |
| 31 #if $charge == 'precursor': | |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
galaxyp
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32 --chg true |
| 0 | 33 #end if |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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34 $rmm $mbr $pro |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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35 --out . > logfile.txt |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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36 && cat logfile.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log' |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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37 && cp *_FlashLFQ_QuantifiedProteins.tsv '$quantifiedProteins' |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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38 && cp *_FlashLFQ_QuantifiedPeptides.tsv '$quantifiedPeptides' |
| 2 | 39 && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks' |
| 0 | 40 ]]></command> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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changeset
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41 |
| 0 | 42 <inputs> |
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9
944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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changeset
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43 <param name="idt" type="data" format="tabular" label="identification file" |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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44 help="MetaMorpheus,Morpheus,PeptideShaker PSM Report,MaxQuant"/> |
| 2 | 45 <param name="peak_lists" type="data" format="mzml" multiple="true" label="spectrum files"/> |
| 0 | 46 <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/> |
| 47 <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/> | |
| 48 <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/> | |
| 49 <param name="intensity" type="select" label="intensity"> | |
| 50 <option value="apex" selected="true">use the apex intensity</option> | |
| 51 <option value="integrate">integrate chromatographic peak intensity</option> | |
| 52 </param> | |
| 53 <param name="charge" type="select" label="charge"> | |
| 54 <option value="all" selected="true">use all identification detected charge states</option> | |
| 55 <option value="precursor">use precursor charge</option> | |
| 56 </param> | |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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57 <param name="rmm" type="boolean" truevalue="--rmm true" falsevalue="--rmm false" checked="true" |
| 2 | 58 label="require observed monoisotopic mass peak"/> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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changeset
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59 <conditional name="normalize"> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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60 <param name="nor" type="select" label="normalize intensity results"> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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61 <option value="false">No</option> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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62 <option value="true">Yes</option> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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63 </param> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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64 <when value="false"/> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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65 <when value="true"> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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66 <param name="experimental_design" type="data" format="tabular" label="ExperimentalDesign.tsv"/> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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67 </when> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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68 </conditional> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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69 <param name="mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false" |
| 2 | 70 label="match between runs"/> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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71 <param name="mrt" type="float" value="1.5" min="0" max="30" label="maximum MBR window in minutes"/> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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72 <param name="pro" type="boolean" truevalue="--pro true" falsevalue="--pro false" checked="false" |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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73 label="advanced protein quantification"/> |
| 0 | 74 </inputs> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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75 |
| 0 | 76 <outputs> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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77 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" /> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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78 <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" /> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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79 <data name="quantifiedPeptides" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeptides.tsv" /> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
galaxyp
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80 <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" /> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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81 |
| 0 | 82 </outputs> |
| 83 <tests> | |
| 84 <test> | |
| 85 <param name="idt" value="aggregatePSMs_5ppmAroundZero.psmtsv" ftype="tabular"/> | |
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41c0c75301b3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty
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86 <param name="peak_lists" value="sliced-mzml.mzML" ftype="mzml"/> |
| 0 | 87 <param name="ppm" value="12"/> |
| 88 <param name="iso" value="6"/> | |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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89 <output name="quantifiedPeaks"> |
| 0 | 90 <assert_contents> |
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944d155c01c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 047addefbac7468a92ba4fc04899bd5136c58ea4
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91 <has_text text="EGFQVADGPLYR" /> |
| 0 | 92 </assert_contents> |
| 93 </output> | |
| 94 </test> | |
| 95 </tests> | |
| 96 <help><![CDATA[ | |
| 97 | |
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279fbc8ad992
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
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98 **FlashLFQ** is an ultrafast label-free quantification for mass-spectrometry proteomics. |
| 0 | 99 |
| 100 **Accepted command-line arguments:** | |
| 101 | |
| 2 | 102 :: |
| 103 | |
| 0 | 104 --idt [string | identification file path (TSV format)] |
| 105 --raw [string | MS data file (.raw or .mzML)] | |
| 106 --rep [string | repository containing MS data files] | |
| 107 --ppm [double | monoisotopic ppm tolerance] (default = 10) | |
| 108 --iso [double | isotopic distribution tolerance in ppm] (default = 5) | |
| 109 --sil [boolean | silent mode; no console output] (default = false) | |
| 110 --pau [boolean | pause at end of run] (default = true) | |
| 111 --int [boolean | integrate chromatographic peak intensity instead of using | |
| 112 the apex intensity] (default = false) | |
| 113 --chg [boolean | use only precursor charge state; when set to false, FlashLFQ looks | |
| 114 for all charge states detected in the MS/MS identification file for each peptide] (default = false) | |
| 115 --mbr [bool|match between runs] | |
| 116 --rmm [bool|require observed monoisotopic mass peak] | |
| 117 --nis [int|number of isotopes required to be observed] | |
| 118 | |
| 119 | |
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41c0c75301b3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty
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120 **Tab-Delimited Identification Text File** |
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41c0c75301b3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty
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121 |
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41c0c75301b3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty
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122 The first line of the text file should contain column headers identifying what each column is. Note that MetaMorpheus (.psmtsv), Morpheus, MaxQuant (msms.txt), and TDPortal tab-delimited column headers are supported natively and such files can be read without modification. For search software that lists decoys and PSMs above 1% FDR (e.g., MetaMorpheus), you may want to remove these prior to FlashLFQ analysis. FlashLFQ will probably crash if ambiguous PSMs are passed into it (e.g., a PSM with more than 2 peptides listed in one line). |
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41c0c75301b3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty
galaxyp
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123 |
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41c0c75301b3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty
galaxyp
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124 The following headers are required in the list of MS/MS identifications: |
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41c0c75301b3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty
galaxyp
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125 |
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41c0c75301b3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 59fca11aabb90cd875d93e7da8791a49e1e2c01a-dirty
galaxyp
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126 - **File Name** - File extensions should be tolerated, but no extension is tested more extensively (e.g. use MyFile and not MyFile.mzML) |
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127 - **Base Sequence** - Should only contain amino acid sequences, or it will likely result in a crash |
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128 - **Full Sequence** - Modified sequence. Can contain any letters, but must be consistent between the same peptidoform to get accurate results |
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129 - **Peptide Monoisotopic Mass** - Theoretical monoisotopic mass, including modification mass |
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130 - **Scan Retention Time** - MS/MS identification scan retention time |
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131 - **Precursor Charge** - Charge of the ion selected for MS/MS resulting in the identification |
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132 - **Protein Accession** - Protein accession(s) for the peptide; protein quantification is still preliminary |
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133 |
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134 |
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135 **Outputs**: |
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136 |
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137 - **QuantifiedProteins.tsv** - Lists protein accession and in the future will include gene and organism if the TSV contains it. The intensity is either a) the sum of the 3 most intense peptides or b) (Advanced protein quant) a weighted-average of the intensities of the peptides assigned to the protein. The weights are determined by how well the peptide co-varies with the other peptides assigned to that protein. |
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138 |
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139 - **QuantifiedPeaks.tsv** - Each chromatographic peak is shown here, even peaks that were not quantifiable (peak intensity = 0). Details about each peak, such as number of PSMs mapped, start/apex/end retention times, ppm error, etc are contained in this file. A peptide can have multiple peaks over the course of a run (e.g., oxidized peptidoforms elute at different times, etc). Ambiguous peaks are displayed with a | (pipe) delimiter to indicate more than one peptide mapped to that peak. |
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140 |
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141 - **QuantifiedPeptides.tsv** - Peptide intensities are summed by modified sequence; this makes it convenient to compare modified peptidoform intensities across runs. |
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142 |
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143 - **Log.txt** - Log of the FlashLFQ run. |
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144 |
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145 |
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146 |
| 0 | 147 ]]></help> |
| 148 <citations> | |
| 149 <citation type="doi">10.1021/acs.jproteome.7b00608</citation> | |
| 150 </citations> | |
| 151 </tool> |