Mercurial > repos > matt-shirley > sra_tools

changeset 20:a1255154fa3f draft

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tweaks to fastq-dump command
author Matt Shirley <mdshw5@gmail.com>
date Mon, 17 Jun 2013 21:41:27 -0400
parents 46adf78139ee
children d850324e82cf
files fastq_dump.xml sra.py
diffstat 2 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_dump.xml	Mon Jun 17 21:28:00 2013 -0400
+++ b/fastq_dump.xml	Mon Jun 17 21:41:27 2013 -0400
@@ -1,6 +1,6 @@
 <tool id="fastq_dump" name="Extract fastq" version="1.0.1">
   <description> format reads from NCBI SRA.</description>
-  <command>fastq-dump --log-level fatal --report never --accession '${input.name}' --stdout $split $aligned '$input' > $output </command>
+  <command>fastq-dump --log-level fatal --accession '${input.name}' --stdout $split $aligned '$input' > $output </command>
   <version_string>fastq-dump --version</version_string>
   <inputs>
     <param format="sra" name="input" type="data" label="sra archive"/>
--- a/sra.py	Mon Jun 17 21:28:00 2013 -0400
+++ b/sra.py	Mon Jun 17 21:41:27 2013 -0400
@@ -1,5 +1,5 @@
 """
-Sra class
+SRA class
 """
 import logging
 import binascii