Mercurial > repos > matt-shirley > sra_tools

changeset 39:1d152e8cb375 draft

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add fastq output option to sam dump
author Matt Shirley <mdshw5@gmail.com>
date Mon, 05 Aug 2013 08:09:27 -0400
parents a0925f507352
children f1b83804013f
files sam_dump.xml
diffstat 1 files changed, 8 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/sam_dump.xml	Sun Aug 04 23:17:53 2013 -0400
+++ b/sam_dump.xml	Mon Aug 05 08:09:27 2013 -0400
@@ -25,6 +25,9 @@
     #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ):
       --primary
     #end if
+    #if str( $fastq ) == "yes":
+      --fastq
+    #end if
     #if $input.input_select == "file":
       $input.file
     #else:
@@ -65,6 +68,11 @@
       <option value="yes">Yes</option>
     </param>
     <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
+    <param format="text" name="fastq" type="select" value="no">
+      <label>output fastq</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
   </inputs>
   <outputs>
     <data format="sam" name="output"/>