| Previous changeset 7:cf494694e8e5 (2019-12-10) Next changeset 9:878f6725c4f3 (2020-01-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 5b42feb3b752fdb22723d6bcedd301b6b1dd8dd3" |
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modified:
flashlfq.xml |
| b |
| diff -r cf494694e8e5 -r 29fe0caf7bca flashlfq.xml --- a/flashlfq.xml Tue Dec 10 13:07:49 2019 -0500 +++ b/flashlfq.xml Wed Jan 08 21:54:15 2020 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="flashlfq" name="FlashLFQ" version="1.0.2.0"> +<tool id="flashlfq" name="FlashLFQ" version="1.0.2.1"> <description>ultrafast label-free quantification for mass-spectrometry proteomics</description> <requirements> <requirement type="package" version="1.0.2">flashlfq</requirement> @@ -39,7 +39,7 @@ #end if $experiment.bayesian.sha $experiment.bayesian.rmc - --mcm '$experiment.bayesian.mcm' + --mcm $experiment.bayesian.mcm #if str($experiment.bayesian.rns): --rns $experiment.bayesian.rns #end if @@ -54,11 +54,11 @@ <param argument="--ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/> <param argument="--iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/> <param argument="--nis" type="integer" value="2" min="2" max="30" label="number of isotopes required to be observed"/> - <param argument="--int" type="boolean" truevalue="--int true" falsevalue="--int false" checked="false" + <param argument="--int" type="boolean" truevalue="--int true" falsevalue="" checked="false" label="integrate peak areas (not recommended)"/> - <param argument="--chg" type="boolean" truevalue="--chg true" falsevalue="--chg false" checked="false" + <param argument="--chg" type="boolean" truevalue="--chg true" falsevalue="" checked="false" label="use only precursor charge state"/> - <param argument="--mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false" + <param argument="--mbr" type="boolean" truevalue="--mbr true" falsevalue="" checked="false" label="match between runs"/> <param argument="--mrt" type="float" value="2.5" min=".01" max="60" label="maximum MBR window in minutes"/> <conditional name="experiment"> @@ -69,7 +69,7 @@ <when value="false"/> <when value="true"> <param name="experimental_design" type="data" format="tabular" label="ExperimentalDesign.tsv"/> - <param argument="--nor" type="boolean" truevalue="--nor true" falsevalue="--nor false" checked="true" + <param argument="--nor" type="boolean" truevalue="--nor true" falsevalue="" checked="true" label="normalize intensity results"/> <conditional name="bayesian"> <param name="calculate" type="select" label="Perform Bayesian protein fold-change analysis"> @@ -89,9 +89,9 @@ </param> <param argument="--fcc" type="float" value="" min="0.01" label="fold-change cutoff" optional="true" help="Leave blank to detemine emperically from data."/> - <param argument="--sha" type="boolean" truevalue="--sha true" falsevalue="--sha false" checked="false" + <param argument="--sha" type="boolean" truevalue="--sha true" falsevalue="" checked="false" label="use shared peptides for protein quantification"/> - <param argument="--rmc" type="boolean" truevalue="--rmc true" falsevalue="--rmc false" checked="false" + <param argument="--rmc" type="boolean" truevalue="--rmc true" falsevalue="" checked="false" label="require MS/MS ID in condition"/> <param argument="--mcm" type="integer" value="500" min="500" label="number of markov-chain monte carlo iterations"/> <param argument="--rns" type="integer" value="" optional="true" label="random seed"/> |