Mercurial > repos > galaxyp > flashlfq
changeset 5:cb346052c5de draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7f1c24d169a610aa910ca717fd698fe782b42699"
| author | galaxyp |
|---|---|
| date | Thu, 24 Oct 2019 15:51:49 -0400 |
| parents | 908ab13490dc |
| children | c8ae97f37bf3 |
| files | flashlfq.xml |
| diffstat | 1 files changed, 132 insertions(+), 61 deletions(-) [+] |
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--- a/flashlfq.xml Wed Jan 30 05:39:17 2019 -0500 +++ b/flashlfq.xml Thu Oct 24 15:51:49 2019 -0400 @@ -1,7 +1,7 @@ -<tool id="flashlfq" name="FlashLFQ" version="0.1.111"> +<tool id="flashlfq" name="FlashLFQ" version="1.0.0.0"> <description>ultrafast label-free quantification for mass-spectrometry proteomics</description> <requirements> - <requirement type="package" version="0.1.111">flashlfq</requirement> + <requirement type="package" version="1.0.0">flashlfq</requirement> </requirements> <command><![CDATA[ #import re @@ -9,76 +9,107 @@ ln -s '${idt}' '${idt_path}' && mkdir spectrum_dir && #for $peak_list in $peak_lists: - #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML" + #set $ext = '.mzML' + #if $peak_list.extension.endswith('raw') + #set $ext = '.RAW' + #end if + #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + $ext ln -s '${peak_list}' 'spectrum_dir/${input_name}' && #end for - #if $normalize.nor == 'true': - #set $input_name = $re.sub('[.][^.]*$','',$experimental_design.display_name.split('/')[-1]) + ".tsv" - ln -s '${experimental_design}' 'spectrum_dir/${input_name}' && + #if $experiment.use_design == 'true': + ln -s '${experiment.experimental_design}' 'spectrum_dir/ExperimentalDesign.tsv' && #end if + echo 'y' | FlashLFQ --idt '$idt_path' --rep "./spectrum_dir" --ppm $ppm --iso $iso --nis $nis - #if $normalize.nor == 'true': - --nor true - #end if - #if $intensity == 'integrate': - --int true - #end if - #if $charge == 'precursor': - --chg true + $int + $chg + $mbr + #if $experiment.use_design == 'true': + $experiment.nor + #if $experiment.bayesian.calculate == 'true': + --bay true + --ctr '$experiment.bayesian.ctr' + #if str($experiment.bayesian.fcc): + -fcc $experiment.bayesian.fcc + #end if + $experiment.bayesian.sha + $experiment.bayesian.rmc + --mcm '$experiment.bayesian.mcm' + #if str($experiment.bayesian.rns): + --rns $experiment.bayesian.rns + #end if + #end if #end if - $rmm $mbr $pro - --out . > logfile.txt - && cat logfile.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log' - && cp *_FlashLFQ_QuantifiedProteins.tsv '$quantifiedProteins' - && cp *_FlashLFQ_QuantifiedPeptides.tsv '$quantifiedPeptides' - && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks' + --out out > logfile.txt ]]></command> - <inputs> - <param name="idt" type="data" format="tabular" label="identification file" + <param argument="--idt" type="data" format="tabular" label="identification file" help="MetaMorpheus,Morpheus,PeptideShaker PSM Report,MaxQuant"/> - <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"/> - <param name="intensity" type="select" label="intensity"> - <option value="apex" selected="true">use the apex intensity</option> - <option value="integrate">integrate chromatographic peak intensity</option> - </param> - <param name="charge" type="select" label="charge"> - <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"/> - <conditional name="normalize"> - <param name="nor" type="select" label="normalize intensity results"> + <param name="peak_lists" type="data" format="mzml,raw,thermo.raw" multiple="true" label="spectrum files"/> + <param argument="--ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/> + <param argument="--iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/> + <param argument="--nis" type="integer" value="2" min="2" max="30" label="number of isotopes required to be observed"/> + <param argument="--int" type="boolean" truevalue="--int true" falsevalue="--int false" checked="false" + label="integrate peak areas (not recommended)"/> + <param argument="--chg" type="boolean" truevalue="--chg true" falsevalue="--chg false" checked="false" + label="use only precursor charge state"/> + <param argument="--mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false" + label="match between runs"/> + <param argument="--mrt" type="float" value="2.5" min=".01" max="60" label="maximum MBR window in minutes"/> + <conditional name="experiment"> + <param name="use_design" type="select" label="Use experimnetal design for normalization or protein fold-change analysis"> <option value="false">No</option> <option value="true">Yes</option> </param> <when value="false"/> <when value="true"> <param name="experimental_design" type="data" format="tabular" label="ExperimentalDesign.tsv"/> + <param argument="--nor" type="boolean" truevalue="--nor true" falsevalue="--nor false" checked="true" + label="normalize intensity results"/> + <conditional name="bayesian"> + <param name="calculate" type="select" label="Perform Bayesian protein fold-change analysis"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false"/> + <when value="true"> + <param argument="--ctr" type="select" value="" label="control condition for Bayesian protein fold-change analysis"> + <options from_dataset="experimental_design"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="static_value" name="heading_ctr" column="1" value="Condition" keep="False"/> + <filter type="unique_value" name="unique_ctr" column="1"/> + <filter type="sort_by" name="sorted_ctr" column="1"/> + </options> + </param> + <param argument="--fcc" type="float" value="" min="0.01" label="fold-change cutoff" optional="true" + help="Leave blank to detemine emperically from data."/> + <param argument="--sha" type="boolean" truevalue="--sha true" falsevalue="--sha false" checked="false" + label="use shared peptides for protein quantification"/> + <param argument="--rmc" type="boolean" truevalue="--rmc true" falsevalue="--rmc false" checked="false" + label="require MS/MS ID in condition"/> + <param argument="--mcm" type="integer" value="500" min="500" label="number of markov-chain monte carlo iterations"/> + <param argument="--rns" type="integer" value="" optional="true" label="random seed"/> + </when> + </conditional> </when> </conditional> - <param name="mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false" - label="match between runs"/> - <param name="mrt" type="float" value="1.5" min="0" max="30" label="maximum MBR window in minutes"/> - <param name="pro" type="boolean" truevalue="--pro true" falsevalue="--pro false" checked="false" - label="advanced protein quantification"/> </inputs> <outputs> - <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" /> - <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" /> - <data name="quantifiedPeptides" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeptides.tsv" /> - <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" /> - + <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="logfile.txt"/> + <data name="toml" format="txt" label="${tool.name} on ${on_string}: FlashLfqSettings.toml" from_work_dir="out/FlashLfqSettings.toml"/> + <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" from_work_dir="out/QuantifiedPeaks.tsv"/> + <data name="quantifiedPeptides" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeptides.tsv" from_work_dir="out/QuantifiedPeptides.tsv"/> + <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" from_work_dir="out/QuantifiedProteins.tsv"/> + <data name="foldChange" format="tabular" label="${tool.name} on ${on_string}: BayesianFoldChangeAnalysis.tsv" from_work_dir="out/BayesianFoldChangeAnalysis.tsv"> + <filter>'bayesian' in experiment and 'ctr' in experiment['bayesian']</filter> + </data> </outputs> <tests> <test> @@ -94,27 +125,38 @@ </test> </tests> <help><![CDATA[ +**FlashLFQ** is an ultrafast label-free quantification for mass-spectrometry proteomics. +https://github.com/smith-chem-wisc/FlashLFQ/wiki -**FlashLFQ** is an ultrafast label-free quantification for mass-spectrometry proteomics. **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) + --idt [string|identification file path] + --rep [string|directory containing spectral data files] + --out [string|output directory] + --ppm [double|ppm tolerance] + --nor [bool|normalize intensity results] --mbr [bool|match between runs] - --rmm [bool|require observed monoisotopic mass peak] + --sha [bool|use shared peptides for protein quantification] + --bay [bool|Bayesian protein fold-change analysis] + --ctr [string|control condition for Bayesian protein fold-change analysis] + --fcc [double|fold-change cutoff for Bayesian protein fold-change analysis] + +**Advanced settings:** + +:: + + --sil [bool|silent mode] + --int [bool|integrate peak areas (not recommended)] + --iso [double|isotopic distribution tolerance in ppm] + --mrt [double|maximum MBR window in minutes] + --chg [bool|use only precursor charge state] --nis [int|number of isotopes required to be observed] + --rmc [bool|require MS/MS ID in condition] + --mcm [int|number of markov-chain monte carlo iterations for the Bayesian protein fold-change analysis] + --rns [int|random seed for the Bayesian protein fold-change analysis] **Tab-Delimited Identification Text File** @@ -131,6 +173,33 @@ - **Precursor Charge** - Charge of the ion selected for MS/MS resulting in the identification - **Protein Accession** - Protein accession(s) for the peptide; protein quantification is still preliminary +**ExperimentalDesign File** + +The ExperimentalDesign_ File should have 5 columns separated by TAB characters: + + - SpectrumFileName - Without the file extension + - Condition - Cannot be blank + - Sample - an integer, at least 1. Each condition must have continuous sample numbers starting at 1. For example, samples 1, 3, and 4 are not valid because sample 2 is missing. In this case you would label the samples as 1, 2, and 3. + - Fraction - an integer, at least 1. Each sample must have continuous fraction numbers starting at 1. If your data is not fractionated, just enter 1 for all fractions. It is OK for two samples to have different total numbers of fractions. It is NOT recommended to use a sample if it is missing a fraction with significant peptide intensity (e.g., if sample 2 is missing fraction #5 out of 10 total fractions). + - Replicate - an integer, at least 1. Each fraction must have continuous replicate numbers starting at 1. + +:: + + For example, with spectrum files named: + + - 20130510_EXQ1_IgPa_QC_UPS1_01.mzml + - 20130510_EXQ1_IgPa_QC_UPS1_02.mzml + - 20130510_EXQ1_IgPa_QC_UPS2_01.mzml + - 20130510_EXQ1_IgPa_QC_UPS2_02.mzml + + The ExperimentalDesign File: + + FileName Condition Biorep Fraction Techrep + 20130510_EXQ1_IgPa_QC_UPS1_01 S1 1 1 1 + 20130510_EXQ1_IgPa_QC_UPS1_02 S1 2 1 1 + 20130510_EXQ1_IgPa_QC_UPS2_01 S2 1 1 1 + 20130510_EXQ1_IgPa_QC_UPS2_02 S2 2 1 1 + **Outputs**: @@ -143,6 +212,8 @@ - **Log.txt** - Log of the FlashLFQ run. +.. _FlashLFQ: https://github.com/smith-chem-wisc/FlashLFQ/wiki +.. _ExperimentalDesign: https://github.com/smith-chem-wisc/FlashLFQ/wiki/Experimental-Design ]]></help> <citations>