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comparison flashlfq.xml @ 5:3b0c2e1927c1 draft

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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
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4:597199e75dcc 5:3b0c2e1927c1
1 <tool id="flashlfq" name="FlashLFQ" version="0.1.99"> 1 <tool id="flashlfq" name="FlashLFQ" version="0.1.0">
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 ln -s '${idt}' '${idt_path}' && 9 mkdir spectrum_dir;
10 ln -s '${idt}' '${idt_path}';
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/${input_name}';
13 #end for 14 #end for
14 15 FlashLFQ --idt '$idt_path' --rep spectrum_dir --ppm $ppm --iso $iso --nis $nis
15 FlashLFQ
16 --idt '$idt_path'
17 --rep `pwd`
18 --ppm $ppm
19 --iso $iso
20 --nis $nis
21 #if $intensity == 'integrate': 16 #if $intensity == 'integrate':
22 --int true 17 --int true
23 #end if 18 #end if
24 #if $charge == 'precursor': 19 #if $charge == 'precursor':
25 --chg true 20 --chg true
26 #end if 21 #end if
27 $rmm $mbr 22 $rmm $mbr
28 --pau false 23 --pau false
29 && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log' 24 && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log'
30 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences' 25 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences'
93 </output> 88 </output>
94 </test> 89 </test>
95 </tests> 90 </tests>
96 <help><![CDATA[ 91 <help><![CDATA[
97 92
98 **FlashLFQ** is an ultrafast label-free quantification for mass-spectrometry proteomics. 93 **FlashLFQ**
99 94
100 **Accepted command-line arguments:** 95 **Accepted command-line arguments:**
101 96
102 :: 97 ::
103 98