Mercurial > repos > galaxyp > flashlfq
changeset 5:3b0c2e1927c1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 8b11559f7c02a4a686af1086740795ace14d077d-dirty
author | galaxyp |
---|---|
date | Thu, 25 Jan 2018 16:40:02 -0500 |
parents | 597199e75dcc |
children | 279fbc8ad992 |
files | flashlfq.xml |
diffstat | 1 files changed, 8 insertions(+), 13 deletions(-) [+] |
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--- a/flashlfq.xml Thu Jan 25 16:10:39 2018 -0500 +++ b/flashlfq.xml Thu Jan 25 16:40:02 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="flashlfq" name="FlashLFQ" version="0.1.99"> +<tool id="flashlfq" name="FlashLFQ" version="0.1.0"> <description>ultrafast label-free quantification for mass-spectrometry proteomics</description> <requirements> <requirement type="package" version="0.1.99">flashlfq</requirement> @@ -6,23 +6,18 @@ <command><![CDATA[ #import re #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv" - ln -s '${idt}' '${idt_path}' && + mkdir spectrum_dir; + 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}' '${input_name}' && + ln -s '${peak_list}' 'spectrum_dir/${input_name}'; #end for - - FlashLFQ - --idt '$idt_path' - --rep `pwd` - --ppm $ppm - --iso $iso - --nis $nis + FlashLFQ --idt '$idt_path' --rep spectrum_dir --ppm $ppm --iso $iso --nis $nis #if $intensity == 'integrate': - --int true + --int true #end if #if $charge == 'precursor': - --chg true + --chg true #end if $rmm $mbr --pau false @@ -95,7 +90,7 @@ </tests> <help><![CDATA[ -**FlashLFQ** is an ultrafast label-free quantification for mass-spectrometry proteomics. +**FlashLFQ** **Accepted command-line arguments:**