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comparison flashlfq.xml @ 4:597199e75dcc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 7fafb40376213a4c59322517e6a6aaac38d7e376
author galaxyp
date Thu, 25 Jan 2018 16:10:39 -0500
parents 41c0c75301b3
children 3b0c2e1927c1
comparison
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3:41c0c75301b3 4:597199e75dcc
1 <tool id="flashlfq" name="FlashLFQ" version="0.1.0"> 1 <tool id="flashlfq" name="FlashLFQ" version="0.1.99">
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="0.1.99">flashlfq</requirement> 4 <requirement type="package" version="0.1.99">flashlfq</requirement>
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 ## cp '${idt}' '${idt_path}'; 9 ln -s '${idt}' '${idt_path}' &&
10 ln -s '${idt}' '${idt_path}';
11 #for $peak_list in $peak_lists: 10 #for $peak_list in $peak_lists:
12 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML" 11 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML"
13 ln -s '${peak_list}' '${input_name}'; 12 ln -s '${peak_list}' '${input_name}' &&
14 #end for 13 #end for
15 FlashLFQ --idt '$idt_path' --rep `pwd` --ppm $ppm --iso $iso --nis $nis 14
15 FlashLFQ
16 --idt '$idt_path'
17 --rep `pwd`
18 --ppm $ppm
19 --iso $iso
20 --nis $nis
16 #if $intensity == 'integrate': 21 #if $intensity == 'integrate':
17 --int true 22 --int true
18 #end if 23 #end if
19 #if $charge == 'precursor': 24 #if $charge == 'precursor':
20 --chg true 25 --chg true
21 #end if 26 #end if
22 $rmm $mbr 27 $rmm $mbr
23 --pau false 28 --pau false
24 && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log' 29 && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log'
25 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences' 30 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences'
88 </output> 93 </output>
89 </test> 94 </test>
90 </tests> 95 </tests>
91 <help><![CDATA[ 96 <help><![CDATA[
92 97
93 **FlashLFQ** 98 **FlashLFQ** is an ultrafast label-free quantification for mass-spectrometry proteomics.
94 99
95 **Accepted command-line arguments:** 100 **Accepted command-line arguments:**
96 101
97 :: 102 ::
98 103