diff shuffleBed.xml @ 26:c0fbce5dc84a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811

--- a/shuffleBed.xml	Wed Sep 14 17:29:56 2016 -0400
+++ b/shuffleBed.xml	Mon Oct 17 10:13:20 2016 -0400
@@ -8,8 +8,8 @@
     <command>
 <![CDATA[
         bedtools shuffle
-        -g $genome
-        -i $inputA
+        -g '$genome'
+        -i '$inputA'
         $bedpe
         #if str($seed.seed_choose) == "True":
             -seed $seed.seed
@@ -25,14 +25,14 @@
         $no_overlap
         $allow_beyond
         -maxTries $maxtries
-        > $output
+        > '$output'
 ]]>
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param name="bedpe" type="boolean" label="The file is in BEDPE format" selected="False" truevalue="-bedpe" falsevalue="" />
+        <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" />
         <expand macro="genome" />
-        <param name="chrom" type="boolean" selected="False" truevalue="-chrom" falsevalue=""
+        <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue=""
             label="Keep features in the input file on the same chromosome"
             help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" />
         <expand macro="seed" />
@@ -51,14 +51,14 @@
                 <param name="incl" type="data" format="bed" label="Choose File" />
             </when>
         </conditional>
-        <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue="" 
+        <param name="chromfirst" type="boolean" checked="False" truevalue="-chromFirst" falsevalue="" 
             label="Choose chromosome first"
             help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size. (-chromFirst)" />
         <param name="maxtries" type="integer" value="1000"
             label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" />
-        <param name="no_overlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue=""
+        <param name="no_overlap" type="boolean" checked="False" truevalue="-noOverlapping" falsevalue=""
             label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" />
-        <param name="allow_beyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue=""
+        <param name="allow_beyond" type="boolean" checked="False" truevalue="-allowBeyondChromEnd" falsevalue=""
             label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" />
     </inputs>
     <outputs>