Mercurial > repos > galaxyp > flashlfq

comparison flashlfq.xml @ 8:29fe0caf7bca draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 5b42feb3b752fdb22723d6bcedd301b6b1dd8dd3"
author galaxyp
date Wed, 08 Jan 2020 21:54:15 -0500
parents cf494694e8e5
children 878f6725c4f3
comparison
equal deleted inserted replaced
7:cf494694e8e5 8:29fe0caf7bca
1 <tool id="flashlfq" name="FlashLFQ" version="1.0.2.0"> 1 <tool id="flashlfq" name="FlashLFQ" version="1.0.2.1">
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="1.0.2">flashlfq</requirement> 4 <requirement type="package" version="1.0.2">flashlfq</requirement>
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <command><![CDATA[
37 #if str($experiment.bayesian.fcc): 37 #if str($experiment.bayesian.fcc):
38 --fcc $experiment.bayesian.fcc 38 --fcc $experiment.bayesian.fcc
39 #end if 39 #end if
40 $experiment.bayesian.sha 40 $experiment.bayesian.sha
41 $experiment.bayesian.rmc 41 $experiment.bayesian.rmc
42 --mcm '$experiment.bayesian.mcm' 42 --mcm $experiment.bayesian.mcm
43 #if str($experiment.bayesian.rns): 43 #if str($experiment.bayesian.rns):
44 --rns $experiment.bayesian.rns 44 --rns $experiment.bayesian.rns
45 #end if 45 #end if
46 #end if 46 #end if
47 #end if 47 #end if
52 help="MetaMorpheus,Morpheus,PeptideShaker PSM Report,MaxQuant"/> 52 help="MetaMorpheus,Morpheus,PeptideShaker PSM Report,MaxQuant"/>
53 <param name="peak_lists" type="data" format="mzml,raw,thermo.raw" multiple="true" label="spectrum files"/> 53 <param name="peak_lists" type="data" format="mzml,raw,thermo.raw" multiple="true" label="spectrum files"/>
54 <param argument="--ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/> 54 <param argument="--ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>
55 <param argument="--iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/> 55 <param argument="--iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>
56 <param argument="--nis" type="integer" value="2" min="2" max="30" label="number of isotopes required to be observed"/> 56 <param argument="--nis" type="integer" value="2" min="2" max="30" label="number of isotopes required to be observed"/>
57 <param argument="--int" type="boolean" truevalue="--int true" falsevalue="--int false" checked="false" 57 <param argument="--int" type="boolean" truevalue="--int true" falsevalue="" checked="false"
58 label="integrate peak areas (not recommended)"/> 58 label="integrate peak areas (not recommended)"/>
59 <param argument="--chg" type="boolean" truevalue="--chg true" falsevalue="--chg false" checked="false" 59 <param argument="--chg" type="boolean" truevalue="--chg true" falsevalue="" checked="false"
60 label="use only precursor charge state"/> 60 label="use only precursor charge state"/>
61 <param argument="--mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false" 61 <param argument="--mbr" type="boolean" truevalue="--mbr true" falsevalue="" checked="false"
62 label="match between runs"/> 62 label="match between runs"/>
63 <param argument="--mrt" type="float" value="2.5" min=".01" max="60" label="maximum MBR window in minutes"/> 63 <param argument="--mrt" type="float" value="2.5" min=".01" max="60" label="maximum MBR window in minutes"/>
64 <conditional name="experiment"> 64 <conditional name="experiment">
65 <param name="use_design" type="select" label="Use experimnetal design for normalization or protein fold-change analysis"> 65 <param name="use_design" type="select" label="Use experimnetal design for normalization or protein fold-change analysis">
66 <option value="false">No</option> 66 <option value="false">No</option>
67 <option value="true">Yes</option> 67 <option value="true">Yes</option>
68 </param> 68 </param>
69 <when value="false"/> 69 <when value="false"/>
70 <when value="true"> 70 <when value="true">
71 <param name="experimental_design" type="data" format="tabular" label="ExperimentalDesign.tsv"/> 71 <param name="experimental_design" type="data" format="tabular" label="ExperimentalDesign.tsv"/>
72 <param argument="--nor" type="boolean" truevalue="--nor true" falsevalue="--nor false" checked="true" 72 <param argument="--nor" type="boolean" truevalue="--nor true" falsevalue="" checked="true"
73 label="normalize intensity results"/> 73 label="normalize intensity results"/>
74 <conditional name="bayesian"> 74 <conditional name="bayesian">
75 <param name="calculate" type="select" label="Perform Bayesian protein fold-change analysis"> 75 <param name="calculate" type="select" label="Perform Bayesian protein fold-change analysis">
76 <option value="false">No</option> 76 <option value="false">No</option>
77 <option value="true">Yes</option> 77 <option value="true">Yes</option>
87 <filter type="sort_by" name="sorted_ctr" column="1"/> 87 <filter type="sort_by" name="sorted_ctr" column="1"/>
88 </options> 88 </options>
89 </param> 89 </param>
90 <param argument="--fcc" type="float" value="" min="0.01" label="fold-change cutoff" optional="true" 90 <param argument="--fcc" type="float" value="" min="0.01" label="fold-change cutoff" optional="true"
91 help="Leave blank to detemine emperically from data."/> 91 help="Leave blank to detemine emperically from data."/>
92 <param argument="--sha" type="boolean" truevalue="--sha true" falsevalue="--sha false" checked="false" 92 <param argument="--sha" type="boolean" truevalue="--sha true" falsevalue="" checked="false"
93 label="use shared peptides for protein quantification"/> 93 label="use shared peptides for protein quantification"/>
94 <param argument="--rmc" type="boolean" truevalue="--rmc true" falsevalue="--rmc false" checked="false" 94 <param argument="--rmc" type="boolean" truevalue="--rmc true" falsevalue="" checked="false"
95 label="require MS/MS ID in condition"/> 95 label="require MS/MS ID in condition"/>
96 <param argument="--mcm" type="integer" value="500" min="500" label="number of markov-chain monte carlo iterations"/> 96 <param argument="--mcm" type="integer" value="500" min="500" label="number of markov-chain monte carlo iterations"/>
97 <param argument="--rns" type="integer" value="" optional="true" label="random seed"/> 97 <param argument="--rns" type="integer" value="" optional="true" label="random seed"/>
98 </when> 98 </when>
99 </conditional> 99 </conditional>