diff flashlfq.xml @ 8:29fe0caf7bca draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 5b42feb3b752fdb22723d6bcedd301b6b1dd8dd3"

--- a/flashlfq.xml	Tue Dec 10 13:07:49 2019 -0500
+++ b/flashlfq.xml	Wed Jan 08 21:54:15 2020 -0500
@@ -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"/>