Mercurial > repos > galaxyp > flashlfq
changeset 2:d042eabcd6ec draft
Uploaded
author | galaxyp |
---|---|
date | Wed, 06 Dec 2017 13:46:13 -0500 |
parents | a30802542619 |
children | 41c0c75301b3 |
files | flashlfq.xml |
diffstat | 1 files changed, 25 insertions(+), 18 deletions(-) [+] |
line wrap: on
line diff
--- a/flashlfq.xml Wed Dec 06 09:04:50 2017 -0500 +++ b/flashlfq.xml Wed Dec 06 13:46:13 2017 -0500 @@ -4,18 +4,32 @@ <requirement type="package" version="0.1.99">flashlfq</requirement> </requirements> <command><![CDATA[ - FlashLFQ --idt $idt --rep Test2 --ppm $psm --iso $iso + #import re + #set $idt_path = $re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1]) + ".psmtsv" + ## cp '${idt}' '${idt_path}'; + ln -s '${idt}' '${idt_path}'; + #for $peak_list in $peak_lists: + #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML" + ln -s '${peak_list}' '${input_name}'; + #end for + FlashLFQ --idt $idt_path --rep `pwd` --ppm $ppm --iso $iso --nis $nis #if $intensity == 'integrate': --int true #end if #if $charge == 'precursor': --chg true #end if + $rmm $mbr --pau false + && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log' + && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences' + && cp *_FlashLFQ_QuantifiedModifiedSequences.tsv '$quantifiedModifiedSequences' + && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks' + && cp *_FlashLFQ_QuantifiedProteins.tsv '$quantifiedProteins' ]]></command> <inputs> <param name="idt" type="data" format="tabular" label="identification file"/> - <param name="scans" type="data" format="mzml" multiple="true" label="spectrum files"/> + <param name="peak_lists" type="data" format="mzml" multiple="true" label="spectrum files"/> <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/> <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/> <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/> @@ -27,11 +41,13 @@ <option value="all" selected="true">use all identification detected charge states</option> <option value="precursor">use precursor charge</option> </param> - <!-- - --> + <param name="rmm" type="boolean" truevalue="--rmm true" falsevalue="--rmm false" checked="true" + label="require observed monoisotopic mass peak"/> + <param name="mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false" + label="match between runs"/> </inputs> <outputs> - <data name="log" format="text" label="${tool.name} on ${on_string}: Log" /> + <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" /> <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv" /> <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv" /> <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" /> @@ -45,7 +61,7 @@ <param name="iso" value="6"/> <output name="log"> <assert_contents> - <has_text text="ppmTolerance = 10" /> + <has_text text="ppmTolerance = 12" /> <has_text text="isotopePpmTolerance = 6" /> </assert_contents> </output> @@ -53,34 +69,25 @@ </tests> <help><![CDATA[ - +**FlashLFQ** **Accepted command-line arguments:** +:: + --idt [string | identification file path (TSV format)] - --raw [string | MS data file (.raw or .mzML)] - --rep [string | repository containing MS data files] - --ppm [double | monoisotopic ppm tolerance] (default = 10) - --iso [double | isotopic distribution tolerance in ppm] (default = 5) - --sil [boolean | silent mode; no console output] (default = false) - --pau [boolean | pause at end of run] (default = true) - --int [boolean | integrate chromatographic peak intensity instead of using the apex intensity] (default = false) - --chg [boolean | use only precursor charge state; when set to false, FlashLFQ looks for all charge states detected in the MS/MS identification file for each peptide] (default = false) - --mbr [bool|match between runs] - --rmm [bool|require observed monoisotopic mass peak] - --nis [int|number of isotopes required to be observed]