# HG changeset patch
# User drosofff
# Date 1435093141 14400
# Node ID 5d82f9b15957794a30e4a062dd5187bf8a3ff34f
# Parent  738a39851eae4d761b9417c6100e63675698ade6
planemo upload for repository https://bitbucket.org/drosofff/gedtools/

diff -r 738a39851eae -r 5d82f9b15957 sRbowtie.py
--- a/sRbowtie.py	Thu Jun 11 09:22:04 2015 -0400
+++ b/sRbowtie.py	Tue Jun 23 16:59:01 2015 -0400
@@ -145,7 +145,7 @@
         # |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam -
         # generates an "unsorted.bam.sorted.bam file", NOT an
         # "unsorted.bam.sorted" file
-        second_command_line = "/usr/bin/env samtools sort  %s %s" % (
+        second_command_line = "samtools sort  %s %s" % (
             path_to_unsortedBam, path_to_sortedBam)
         # fileno() method return the file descriptor number of tmp_stderr
         p = subprocess.Popen(
diff -r 738a39851eae -r 5d82f9b15957 sRbowtie.xml
--- a/sRbowtie.xml	Thu Jun 11 09:22:04 2015 -0400
+++ b/sRbowtie.xml	Tue Jun 23 16:59:01 2015 -0400
@@ -55,12 +55,12 @@
             </when>
         </conditional>
         <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select">
-            <option select="true" value="tabular">tabular</option>
+            <option selected="true" value="tabular">tabular</option>
             <option value="sam">sam</option>
             <option value="bam">bam</option>
         </param>
         <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
-            <option select="true" value="No">No</option>
+            <option selected="true" value="No">No</option>
             <option value="al">aligned</option>
             <option value="unal">unaligned</option>
             <option value="al_and_unal">both aligned and unaligned</option>