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comparison flashlfq.xml @ 2:d042eabcd6ec draft

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author galaxyp
date Wed, 06 Dec 2017 13:46:13 -0500
parents a30802542619
children 41c0c75301b3
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1:a30802542619 2:d042eabcd6ec
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 FlashLFQ --idt $idt --rep Test2 --ppm $psm --iso $iso 7 #import re
8 #set $idt_path = $re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1]) + ".psmtsv"
9 ## cp '${idt}' '${idt_path}';
10 ln -s '${idt}' '${idt_path}';
11 #for $peak_list in $peak_lists:
12 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML"
13 ln -s '${peak_list}' '${input_name}';
14 #end for
15 FlashLFQ --idt $idt_path --rep `pwd` --ppm $ppm --iso $iso --nis $nis
8 #if $intensity == 'integrate': 16 #if $intensity == 'integrate':
9 --int true 17 --int true
10 #end if 18 #end if
11 #if $charge == 'precursor': 19 #if $charge == 'precursor':
12 --chg true 20 --chg true
13 #end if 21 #end if
22 $rmm $mbr
14 --pau false 23 --pau false
24 && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log'
25 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences'
26 && cp *_FlashLFQ_QuantifiedModifiedSequences.tsv '$quantifiedModifiedSequences'
27 && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks'
28 && cp *_FlashLFQ_QuantifiedProteins.tsv '$quantifiedProteins'
15 ]]></command> 29 ]]></command>
16 <inputs> 30 <inputs>
17 <param name="idt" type="data" format="tabular" label="identification file"/> 31 <param name="idt" type="data" format="tabular" label="identification file"/>
18 <param name="scans" type="data" format="mzml" multiple="true" label="spectrum files"/> 32 <param name="peak_lists" type="data" format="mzml" multiple="true" label="spectrum files"/>
19 <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/> 33 <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>
20 <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/> 34 <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>
21 <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/> 35 <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/>
22 <param name="intensity" type="select" label="intensity"> 36 <param name="intensity" type="select" label="intensity">
23 <option value="apex" selected="true">use the apex intensity</option> 37 <option value="apex" selected="true">use the apex intensity</option>
25 </param> 39 </param>
26 <param name="charge" type="select" label="charge"> 40 <param name="charge" type="select" label="charge">
27 <option value="all" selected="true">use all identification detected charge states</option> 41 <option value="all" selected="true">use all identification detected charge states</option>
28 <option value="precursor">use precursor charge</option> 42 <option value="precursor">use precursor charge</option>
29 </param> 43 </param>
30 <!-- 44 <param name="rmm" type="boolean" truevalue="--rmm true" falsevalue="--rmm false" checked="true"
31 --> 45 label="require observed monoisotopic mass peak"/>
46 <param name="mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false"
47 label="match between runs"/>
32 </inputs> 48 </inputs>
33 <outputs> 49 <outputs>
34 <data name="log" format="text" label="${tool.name} on ${on_string}: Log" /> 50 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" />
35 <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv" /> 51 <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv" />
36 <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv" /> 52 <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv" />
37 <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" /> 53 <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" />
38 <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" /> 54 <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" />
39 </outputs> 55 </outputs>
43 <param name="scans" value="sliced-mzml.mzML" ftype="mzml"/> 59 <param name="scans" value="sliced-mzml.mzML" ftype="mzml"/>
44 <param name="ppm" value="12"/> 60 <param name="ppm" value="12"/>
45 <param name="iso" value="6"/> 61 <param name="iso" value="6"/>
46 <output name="log"> 62 <output name="log">
47 <assert_contents> 63 <assert_contents>
48 <has_text text="ppmTolerance = 10" /> 64 <has_text text="ppmTolerance = 12" />
49 <has_text text="isotopePpmTolerance = 6" /> 65 <has_text text="isotopePpmTolerance = 6" />
50 </assert_contents> 66 </assert_contents>
51 </output> 67 </output>
52 </test> 68 </test>
53 </tests> 69 </tests>
54 <help><![CDATA[ 70 <help><![CDATA[
55 71
56 72 **FlashLFQ**
57 73
58 **Accepted command-line arguments:** 74 **Accepted command-line arguments:**
59 75
76 ::
77
60 --idt [string | identification file path (TSV format)] 78 --idt [string | identification file path (TSV format)]
61
62 --raw [string | MS data file (.raw or .mzML)] 79 --raw [string | MS data file (.raw or .mzML)]
63
64 --rep [string | repository containing MS data files] 80 --rep [string | repository containing MS data files]
65
66 --ppm [double | monoisotopic ppm tolerance] (default = 10) 81 --ppm [double | monoisotopic ppm tolerance] (default = 10)
67
68 --iso [double | isotopic distribution tolerance in ppm] (default = 5) 82 --iso [double | isotopic distribution tolerance in ppm] (default = 5)
69
70 --sil [boolean | silent mode; no console output] (default = false) 83 --sil [boolean | silent mode; no console output] (default = false)
71
72 --pau [boolean | pause at end of run] (default = true) 84 --pau [boolean | pause at end of run] (default = true)
73
74 --int [boolean | integrate chromatographic peak intensity instead of using 85 --int [boolean | integrate chromatographic peak intensity instead of using
75 the apex intensity] (default = false) 86 the apex intensity] (default = false)
76
77 --chg [boolean | use only precursor charge state; when set to false, FlashLFQ looks 87 --chg [boolean | use only precursor charge state; when set to false, FlashLFQ looks
78 for all charge states detected in the MS/MS identification file for each peptide] (default = false) 88 for all charge states detected in the MS/MS identification file for each peptide] (default = false)
79
80 --mbr [bool|match between runs] 89 --mbr [bool|match between runs]
81
82 --rmm [bool|require observed monoisotopic mass peak] 90 --rmm [bool|require observed monoisotopic mass peak]
83
84 --nis [int|number of isotopes required to be observed] 91 --nis [int|number of isotopes required to be observed]
85 92
86 93
87 ]]></help> 94 ]]></help>
88 <citations> 95 <citations>