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comparison flashlfq.xml @ 10:92c059f90d0e draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a72ed1b1e61e0f948dc36b220d2746dc6f06bccf"
author galaxyp
date Tue, 07 Apr 2020 05:32:03 -0400
parents 878f6725c4f3
children
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9:878f6725c4f3 10:92c059f90d0e
1 <tool id="flashlfq" name="FlashLFQ" version="1.0.3.0"> 1 <tool id="flashlfq" name="FlashLFQ" version="1.0.3.1">
2 <description>ultrafast label-free quantification for mass-spectrometry proteomics</description> 2 <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.3">flashlfq</requirement> 4 <requirement type="package" version="1.0.3">flashlfq</requirement>
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <stdio>
7 <regex match="Problem opening .mzML file" level="fatal" source="stdout" description="Proplem opening mzML file." />
8 </stdio>
9 <command detect_errors="exit_code"><![CDATA[
7 #import re 10 #import re
8 #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv" 11 #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv"
9 ln -s '${idt}' '${idt_path}' && 12 ln -s '${idt}' '${idt_path}' &&
10 mkdir spectrum_dir && 13 mkdir spectrum_dir &&
11 #for $peak_list in $peak_lists: 14 #for $peak_list in $peak_lists:
43 #if str($experiment.bayesian.rns): 46 #if str($experiment.bayesian.rns):
44 --rns $experiment.bayesian.rns 47 --rns $experiment.bayesian.rns
45 #end if 48 #end if
46 #end if 49 #end if
47 #end if 50 #end if
48 --out out > logfile.txt 51 --out out | tee logfile.txt
49 ]]></command> 52 ]]></command>
50 <inputs> 53 <inputs>
51 <param argument="--idt" type="data" format="tabular" label="identification file" 54 <param argument="--idt" type="data" format="tabular" label="identification file"
52 help="MetaMorpheus,Morpheus,PeptideShaker PSM Report,MaxQuant"/> 55 help="MetaMorpheus,Morpheus,PeptideShaker PSM Report,MaxQuant"/>
53 <param name="peak_lists" type="data" format="mzml,raw,thermo.raw" multiple="true" label="spectrum files"/> 56 <param name="peak_lists" type="data" format="mzml,raw,thermo.raw" multiple="true" label="spectrum files"/>