Mercurial > repos > lomereiter > sambamba_filter

diff sambamba_filter.xml @ 5:123168c85390

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updated to 0.4.7; use precompiled binaries
author lomereiter <lomereiter@gmail.com>
date Tue, 04 Nov 2014 18:34:37 +0300
parents a03e95059256
children
line wrap: on
line diff
--- a/sambamba_filter.xml	Wed Jul 24 13:33:50 2013 -0400
+++ b/sambamba_filter.xml	Tue Nov 04 18:34:37 2014 +0300
@@ -1,6 +1,6 @@
-<tool id="sambamba_filter" name="Filter BAM or SAM" version="1.0">
+<tool id="sambamba_filter" name="Filter BAM or SAM" version="1.1">
     <requirements>
-        <requirement type="package" version="0.3.3">sambamba</requirement>
+        <requirement type="package" version="0.4.7">sambamba</requirement>
     </requirements>
     <description>
         on flags, fields, and tags using Sambamba
@@ -20,7 +20,7 @@
         #set $input1 = 'input.bam'
         ln -s $input $input1 &amp;&amp;
         ln -s $input.metadata.bam_index input.bai &amp;&amp;
-        sambamba view 
+        sambamba view -t \${GALAXY_SLOTS:-8}
         #if $query != "":
             --filter="$query"
         #end if
@@ -71,8 +71,6 @@
 Filter Syntax 
 =============
 
-Complete documentation of filter syntax is available at https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax.
-
 A *filter expression* is a number of *basic conditions* linked by ``and``, ``or``, ``not`` logical operators, and enclosed in parentheses where needed.
 
 *Basic condition* is a one for a single record field, tag, or flag.
@@ -157,7 +155,6 @@
 -----
 
 .. _sambamba: http://github.com/lomereiter/sambamba
-.. _filter-syntax: https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax
 
     </help>
 </tool>