Mercurial > repos > galaxyp > flashlfq

comparison flashlfq.xml @ 0:8489cc343cde draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author galaxyp
date Wed, 06 Dec 2017 08:54:47 -0500
parents
children a30802542619
comparison
equal deleted inserted replaced
-1:000000000000 0:8489cc343cde
1 <tool id="flashlfq" name="FlashLFQ" version="0.1.0">
2 <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
3 <requirements>
4 <requirement type="package" version="0.199.0">flashlfq</requirement>
5 </requirements>
6 <command><![CDATA[
7 FlashLFQ --idt $idt --rep Test2 --ppm $psm --iso $iso
8 #if $intensity == 'integrate':
9 --int true
10 #end if
11 #if $charge == 'precursor':
12 --chg true
13 #end if
14 --pau false
15 ]]></command>
16 <inputs>
17 <param name="idt" type="data" format="tabular" label="identification file"/>
18 <param name="scans" type="data" format="mzml" multiple="true" label="spectrum files"/>
19 <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>
20 <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>
21 <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/>
22 <param name="intensity" type="select" label="intensity">
23 <option value="apex" selected="true">use the apex intensity</option>
24 <option value="integrate">integrate chromatographic peak intensity</option>
25 </param>
26 <param name="charge" type="select" label="charge">
27 <option value="all" selected="true">use all identification detected charge states</option>
28 <option value="precursor">use precursor charge</option>
29 </param>
30 <!--
31 -->
32 </inputs>
33 <outputs>
34 <data name="log" format="text" label="${tool.name} on ${on_string}: Log" />
35 <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv" />
36 <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv" />
37 <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" />
38 <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" />
39 </outputs>
40 <tests>
41 <test>
42 <param name="idt" value="aggregatePSMs_5ppmAroundZero.psmtsv" ftype="tabular"/>
43 <param name="scans" value="sliced-mzml.mzML" ftype="mzml"/>
44 <param name="ppm" value="12"/>
45 <param name="iso" value="6"/>
46 <output name="log">
47 <assert_contents>
48 <has_text text="ppmTolerance = 10" />
49 <has_text text="isotopePpmTolerance = 6" />
50 </assert_contents>
51 </output>
52 </test>
53 </tests>
54 <help><![CDATA[
55
56
57
58 **Accepted command-line arguments:**
59
60 --idt [string | identification file path (TSV format)]
61
62 --raw [string | MS data file (.raw or .mzML)]
63
64 --rep [string | repository containing MS data files]
65
66 --ppm [double | monoisotopic ppm tolerance] (default = 10)
67
68 --iso [double | isotopic distribution tolerance in ppm] (default = 5)
69
70 --sil [boolean | silent mode; no console output] (default = false)
71
72 --pau [boolean | pause at end of run] (default = true)
73
74 --int [boolean | integrate chromatographic peak intensity instead of using
75 the apex intensity] (default = false)
76
77 --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)
79
80 --mbr [bool|match between runs]
81
82 --rmm [bool|require observed monoisotopic mass peak]
83
84 --nis [int|number of isotopes required to be observed]
85
86
87 ]]></help>
88 <citations>
89 <citation type="doi">10.1021/acs.jproteome.7b00608</citation>
90 </citations>
91 </tool>