--- a/sam_dump.xml	Mon Mar 30 22:40:59 2015 -0400
+++ b/sam_dump.xml	Wed Apr 01 12:35:38 2015 -0400
@@ -1,7 +1,7 @@
 <tool id="sam_dump" name="Extract reads" version="1.1.2">
   <description> in SAM format from NCBI SRA.</description>
   <command>
-    sam-dump --log-level fatal
+    sam-dump --log-level fatal --disable-multithreading
     #if str( $region ) != "":
       --aligned-region $region
     #end if
@@ -11,7 +11,7 @@
     #if str( $minMapq ) != "":
       --minmapq $minMapq
     #end if
-    #if $header == "yes":
+    #if str( $header ) == "yes":
       --header
     #else:
       --no-header
@@ -25,15 +25,10 @@
     #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
     #elif $input.input_select == "accession_number":
       $input.accession
-    #elif $input.input_select == "text":
-      `cat $input.text`
     #end if
     > $output
   </command>
@@ -43,7 +38,6 @@
       <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"/>
@@ -51,12 +45,9 @@
       <when value="accession_number">
         <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"/>
-    <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/>
+    <param format="text" name="region" type="text" label="aligned region (chr:start-end)"/>
+    <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to)"/>
     <param format="text" name="header" type="select" value="yes">
       <label>output SAM header</label>
       <option value="yes">Yes</option>
@@ -74,26 +65,25 @@
       <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 name="output" format="sam">
-      <change_format>
-        <when input="fastq" value="yes" format="fastq"/>
-      </change_format>
-    </data>
+    <data name="output" format="sam"/>
   </outputs>
   <requirements>
     <requirement type="package" version="2.4.5">sra_toolkit</requirement>
   </requirements>
+  <tests>
+    <test>
+      <param name="input_select" value="accession_number"/>
+      <param name="accession" value="SRR925743"/>
+      <param name="region" value="17:41243452-41277500"/>
+      <output name="output" file="sam_dump_result.sam" ftype="sam" />
+    </test>
+  </tests>
   <help>
-    This tool extracts reads from sra archives using sam-dump.
-    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
-    The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-    Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
+      This tool extracts reads from sra archives using sam-dump.
+      Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
+      The sam-dump program is developed at NCBI, and is available at: http://github.com/ncbi/sra-tools
+      Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy.
   </help>
 </tool>