# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1375721643 14400
# Node ID 3cb113532930d0e7e4139e37863b461e978a2512
# Parent  2c4599d594a5bb3813d20a8000ca42a4f5a93784
sea pileup accept text input

diff -r 2c4599d594a5 -r 3cb113532930 sra_pileup.xml
--- a/sra_pileup.xml	Mon Aug 05 11:43:37 2013 -0400
+++ b/sra_pileup.xml	Mon Aug 05 12:54:03 2013 -0400
@@ -9,8 +9,10 @@
     #end if
     #if $input.input_select == "file":
       $input.file
-    #else:
+    #elif $input.input_select == "accession_number":
       $input.accession 
+    #elif $input.input_select == "text":
+      `cat $input.text`
     #end if
     > $output</command>
   <version_string>sra-pileup --version</version_string>
@@ -19,12 +21,16 @@
       <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="data" label="text file"/>
       </when>
     </conditional>
     <param format="text" name="region" type="text" label="aligned region"/>