diff fastq_dump.xml @ 8:558a88cd49e4

bump toolkit versions, old registration path

--- a/fastq_dump.xml	Thu Mar 13 16:08:12 2014 -0400
+++ b/fastq_dump.xml	Thu Mar 13 16:11:04 2014 -0400
@@ -1,14 +1,14 @@
 <tool id="fastq_dump" name="Extract reads" version="1.1.1">
   <description> from NCBI SRA.</description>
   <command>
-    fastq-dump --log-level fatal 
+    fastq-dump --log-level fatal
     #if $input.input_select == "file":
-      --accession '${input.file.name}' 
+      --accession '${input.file.name}'
     #else:
-      --accession $input.accession 
+      --accession $input.accession
     #end if
-    --defline-seq '@\$sn[_\$rn]/\$ri' 
-    --stdout 
+    --defline-seq '@\$sn[_\$rn]/\$ri'
+    --stdout
     #if $split == "yes":
       --split-spot
     #end if
@@ -19,16 +19,16 @@
       --unaligned
     #end if
     #if str( $minID ) != "":
-      --minSpotId $minID 
+      --minSpotId $minID
     #end if
     #if str( $maxID ) != "":
-      --maxSpotId $maxID 
+      --maxSpotId $maxID
     #end if
     #if str( $minlen ) != "":
-      --minReadLen $minlen 
+      --minReadLen $minlen
     #end if
     #if str( $readfilter ) != "":
-      --read-filter $readfilter 
+      --read-filter $readfilter
     #end if
     #if str( $region ) != "":
       --aligned-region $region
@@ -48,7 +48,7 @@
     #if $input.input_select=="file":
       $input.file
     #else:
-        $input.accession 
+        $input.accession
     #end if
     > $output
   </command>
@@ -112,11 +112,11 @@
     <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
   </stdio>
   <requirements>
-    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
+    <requirement type="package" version="2.3.4-2">sra_toolkit</requirement>
   </requirements>
   <help>
-    This tool extracts reads from SRA archives using fastq-dump. 
-    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 
+    This tool extracts reads from SRA archives using fastq-dump.
+    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
     The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
     Contact Matt Shirley at [e-mail] for support and bug reports.
   </help>