# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1372535594 14400
# Node ID 996add6daf368995f18d011e23af4f40d6173c94
# Parent  2295c666e6ce97eeeb46db5a119432ea20c4f90d
debug prefetch caching and accession input for fastq_dump

diff -r 2295c666e6ce -r 996add6daf36 fastq_dump.xml
--- a/fastq_dump.xml	Sat Jun 29 15:49:44 2013 -0400
+++ b/fastq_dump.xml	Sat Jun 29 15:53:14 2013 -0400
@@ -2,7 +2,7 @@
   <description> format reads from NCBI sra.</description>
   <command>
     #if $input.input_select=="file"
-        fastq-dump --log-level fatal --accession '${input.sra.name}' --stdout $split $aligned $input.sra > $output 
+        fastq-dump --log-level fatal --accession '${input.sra.name}' --stdout $split $aligned $input.file > $output 
     #else
         fastq-dump --log-level fatal --accession $input.accession --stdout $split $aligned $input.accession > $output 
     #end if
@@ -15,10 +15,10 @@
         <option value="file">SRA archive in current history</option>
       </param>
       <when value="file">
-	<param format="sra" name="input" type="data" label="sra archive"/>
+	<param format="sra" name="file" type="data" label="sra archive"/>
       </when>
       <when value="accession_number">
-	<param format="text" name="input" type="text" label="accession"/>
+	<param format="text" name="accession" type="text" label="accession"/>
       </when>
     </conditional>
     <param format="text" name="split" type="select" value="">