# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1375710026 14400
# Node ID f1b83804013f65182fc546aea18b487786c059a0
# Parent  1d152e8cb375b349375594e9b3b258d6bb85f226
add option to take plaintext file with accession on one line

diff -r 1d152e8cb375 -r f1b83804013f sam_dump.xml
--- a/sam_dump.xml	Mon Aug 05 08:09:27 2013 -0400
+++ b/sam_dump.xml	Mon Aug 05 09:40:26 2013 -0400
@@ -30,8 +30,10 @@
     #end if
     #if $input.input_select == "file":
       $input.file
-    #else:
+    #elif $input.input_select == "accession_number":
       $input.accession 
+    #elif $input.input_select == "text":
+      $input.text
     #end if
     > $output
   </command>  
@@ -41,12 +43,16 @@
       <param name="input_select" type="select" label="select input type">
         <option value="accession_number">SRR accession</option>
         <option value="file">SRA archive in current history</option>
+        <option value="text">text file containing SRR accession</option>
       </param>
       <when value="file">
-    <param format="sra" name="file" type="data" label="sra archive"/>
+        <param format="sra" name="file" type="data" label="sra archive"/>
       </when>
       <when value="accession_number">
-    <param format="text" name="accession" type="text" label="accession"/>
+        <param format="text" name="accession" type="text" label="accession"/>
+      </when>
+      <when value="text">
+        <param format="txt" name="text" type="txt" label="text file"/>
       </when>
     </conditional>
     <param format="text" name="region" type="text" label="aligned region"/>