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comparison flashlfq.xml @ 1:1e2fc34b1f20 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
author galaxyp
date Thu, 25 Jan 2018 18:02:19 -0500
parents 6d3560a3a548
children e70198847b2a
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0:6d3560a3a548 1:1e2fc34b1f20
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <command><![CDATA[
7 #import re 7 #import re
8 #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv" 8 #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv"
9 ln -s '${idt}' '${idt_path}' && 9 ln -s '${idt}' '${idt_path}' &&
10 mkdir spectrum_dir &&
10 #for $peak_list in $peak_lists: 11 #for $peak_list in $peak_lists:
11 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML" 12 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML"
12 ln -s '${peak_list}' '${input_name}' && 13 ln -s '${peak_list}' 'spectrum_dir/${input_name}' &&
13 #end for 14 #end for
14 15
15 FlashLFQ 16 FlashLFQ
16 --idt '$idt_path' 17 --idt '$idt_path'
17 --rep `pwd` 18 --rep spectrum_dir
18 --ppm $ppm 19 --ppm $ppm
19 --iso $iso 20 --iso $iso
20 --nis $nis 21 --nis $nis
21 #if $intensity == 'integrate': 22 #if $intensity == 'integrate':
22 --int true 23 --int true