| Previous changeset 4:908ab13490dc (2019-01-30) Next changeset 6:c8ae97f37bf3 (2019-12-04) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7f1c24d169a610aa910ca717fd698fe782b42699" |
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modified:
flashlfq.xml |
| b |
| diff -r 908ab13490dc -r cb346052c5de flashlfq.xml --- a/flashlfq.xml Wed Jan 30 05:39:17 2019 -0500 +++ b/flashlfq.xml Thu Oct 24 15:51:49 2019 -0400 |
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| b'@@ -1,7 +1,7 @@\n-<tool id="flashlfq" name="FlashLFQ" version="0.1.111">\n+<tool id="flashlfq" name="FlashLFQ" version="1.0.0.0">\n <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>\n <requirements>\n- <requirement type="package" version="0.1.111">flashlfq</requirement>\n+ <requirement type="package" version="1.0.0">flashlfq</requirement>\n </requirements>\n <command><![CDATA[\n #import re\n@@ -9,76 +9,107 @@\n ln -s \'${idt}\' \'${idt_path}\' &&\n mkdir spectrum_dir &&\n #for $peak_list in $peak_lists:\n- #set $input_name = $re.sub(\'[.][^.]*$\',\'\',$peak_list.display_name.split(\'/\')[-1]) + ".mzML"\n+ #set $ext = \'.mzML\'\n+ #if $peak_list.extension.endswith(\'raw\')\n+ #set $ext = \'.RAW\'\n+ #end if\n+ #set $input_name = $re.sub(\'[.][^.]*$\',\'\',$peak_list.display_name.split(\'/\')[-1]) + $ext\n ln -s \'${peak_list}\' \'spectrum_dir/${input_name}\' &&\n #end for\n- #if $normalize.nor == \'true\':\n- #set $input_name = $re.sub(\'[.][^.]*$\',\'\',$experimental_design.display_name.split(\'/\')[-1]) + ".tsv"\n- ln -s \'${experimental_design}\' \'spectrum_dir/${input_name}\' &&\n+ #if $experiment.use_design == \'true\':\n+ ln -s \'${experiment.experimental_design}\' \'spectrum_dir/ExperimentalDesign.tsv\' &&\n #end if\n+ echo \'y\' | \n FlashLFQ \n --idt \'$idt_path\'\n --rep "./spectrum_dir"\n --ppm $ppm\n --iso $iso\n --nis $nis\n- #if $normalize.nor == \'true\':\n- --nor true\n- #end if\n- #if $intensity == \'integrate\':\n- --int true\n- #end if\n- #if $charge == \'precursor\':\n- --chg true\n+ $int\n+ $chg\n+ $mbr\n+ #if $experiment.use_design == \'true\':\n+ $experiment.nor\n+ #if $experiment.bayesian.calculate == \'true\':\n+ --bay true\n+ --ctr \'$experiment.bayesian.ctr\'\n+ #if str($experiment.bayesian.fcc):\n+ -fcc $experiment.bayesian.fcc\n+ #end if\n+ $experiment.bayesian.sha\n+ $experiment.bayesian.rmc\n+ --mcm \'$experiment.bayesian.mcm\'\n+ #if str($experiment.bayesian.rns):\n+ --rns $experiment.bayesian.rns\n+ #end if\n+ #end if\n #end if\n- $rmm $mbr $pro\n- --out . > logfile.txt\n- && cat logfile.txt | sed \'s/\\(Analysis summary for:\\).*working./\\1 /\' > \'$log\'\n- && cp *_FlashLFQ_QuantifiedProteins.tsv \'$quantifiedProteins\'\n- && cp *_FlashLFQ_QuantifiedPeptides.tsv \'$quantifiedPeptides\'\n- && cp *_FlashLFQ_QuantifiedPeaks.tsv \'$quantifiedPeaks\'\n+ --out out > logfile.txt\n ]]></command>\n-\n <inputs>\n- <param name="idt" type="data" format="tabular" label="identification file"\n+ <param argument="--idt" type="data" format="tabular" label="identification file"\n help="MetaMorpheus,Morpheus,PeptideShaker PSM Report,MaxQuant"/>\n- <param name="peak_lists" type="data" format="mzml" multiple="true" label="spectrum files"/>\n- <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>\n- <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>\n- <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/>\n- <param name="intensity" type="select" label="intensity">\n- <option value="apex" selected="true">use the apex intensity</option>\n- <option value="integrate">integrate chromatographic peak intensity</option>\n- </param>\n- <param name="charge" type="select" label="charge">\n- <option value="all" selected="true">use all identification detected charge st'..b'ne arguments:**\n \n ::\n \n- --idt [string | identification file path (TSV format)]\n- --raw [string | MS data file (.raw or .mzML)]\n- --rep [string | repository containing MS data files]\n- --ppm [double | monoisotopic ppm tolerance] (default = 10)\n- --iso [double | isotopic distribution tolerance in ppm] (default = 5)\n- --sil [boolean | silent mode; no console output] (default = false)\n- --pau [boolean | pause at end of run] (default = true)\n- --int [boolean | integrate chromatographic peak intensity instead of using \n- the apex intensity] (default = false)\n- --chg [boolean | use only precursor charge state; when set to false, FlashLFQ looks \n- for all charge states detected in the MS/MS identification file for each peptide] (default = false)\n+ --idt [string|identification file path]\n+ --rep [string|directory containing spectral data files]\n+ --out [string|output directory]\n+ --ppm [double|ppm tolerance]\n+ --nor [bool|normalize intensity results]\n --mbr [bool|match between runs]\n- --rmm [bool|require observed monoisotopic mass peak]\n+ --sha [bool|use shared peptides for protein quantification]\n+ --bay [bool|Bayesian protein fold-change analysis]\n+ --ctr [string|control condition for Bayesian protein fold-change analysis]\n+ --fcc [double|fold-change cutoff for Bayesian protein fold-change analysis]\n+\n+**Advanced settings:**\n+\n+::\n+\n+ --sil [bool|silent mode]\n+ --int [bool|integrate peak areas (not recommended)]\n+ --iso [double|isotopic distribution tolerance in ppm]\n+ --mrt [double|maximum MBR window in minutes]\n+ --chg [bool|use only precursor charge state]\n --nis [int|number of isotopes required to be observed]\n+ --rmc [bool|require MS/MS ID in condition]\n+ --mcm [int|number of markov-chain monte carlo iterations for the Bayesian protein fold-change analysis]\n+ --rns [int|random seed for the Bayesian protein fold-change analysis]\n \n \n **Tab-Delimited Identification Text File**\n@@ -131,6 +173,33 @@\n - **Precursor Charge** - Charge of the ion selected for MS/MS resulting in the identification\n - **Protein Accession** - Protein accession(s) for the peptide; protein quantification is still preliminary\n \n+**ExperimentalDesign File**\n+\n+The ExperimentalDesign_ File should have 5 columns separated by TAB characters: \n+\n+ - SpectrumFileName - Without the file extension\n+ - Condition - Cannot be blank\n+ - 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.\n+ - 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).\n+ - Replicate - an integer, at least 1. Each fraction must have continuous replicate numbers starting at 1.\n+\n+::\n+\n+ For example, with spectrum files named:\n+\n+ - 20130510_EXQ1_IgPa_QC_UPS1_01.mzml\n+ - 20130510_EXQ1_IgPa_QC_UPS1_02.mzml\n+ - 20130510_EXQ1_IgPa_QC_UPS2_01.mzml\n+ - 20130510_EXQ1_IgPa_QC_UPS2_02.mzml\n+\n+ The ExperimentalDesign File:\n+\n+ FileName\tCondition\tBiorep\tFraction\tTechrep\n+ 20130510_EXQ1_IgPa_QC_UPS1_01\tS1\t1\t1\t1\n+ 20130510_EXQ1_IgPa_QC_UPS1_02\tS1\t2\t1\t1\n+ 20130510_EXQ1_IgPa_QC_UPS2_01\tS2\t1\t1\t1\n+ 20130510_EXQ1_IgPa_QC_UPS2_02\tS2\t2\t1\t1\n+\n \n **Outputs**:\n \n@@ -143,6 +212,8 @@\n - **Log.txt** - Log of the FlashLFQ run. \n \n \n+.. _FlashLFQ: https://github.com/smith-chem-wisc/FlashLFQ/wiki\n+.. _ExperimentalDesign: https://github.com/smith-chem-wisc/FlashLFQ/wiki/Experimental-Design\n \n ]]></help>\n <citations>\n' |