# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1372634438 14400
# Node ID 7803126704c631c6aa3cdfff8506d9f3b69bfaec
# Parent  9ad900168ded71134e19fdd90fe603c445d17cae
exposed many more options for fastq-dump

diff -r 9ad900168ded -r 7803126704c6 fastq_dump.xml
--- a/fastq_dump.xml	Sun Jun 30 16:18:09 2013 -0400
+++ b/fastq_dump.xml	Sun Jun 30 19:20:38 2013 -0400
@@ -1,11 +1,31 @@
 <tool id="fastq_dump" name="Extract fastq" version="1.0.3">
   <description> format reads from NCBI sra.</description>
   <command>
-    #if $input.input_select=="file"
-        fastq-dump --log-level fatal --accession '${input.file.name}' --stdout $split $aligned $input.file > $output 
-    #else
-        fastq-dump --log-level fatal $input.accession > $output 
+    fastq-dump --log-level fatal 
+    #if $input.input_select == "file":
+      --accession '${input.file.name}' 
+    #else:
+      --accession $input.accession 
     #end if
+    --stdout 
+    $split 
+    $aligned 
+    #if str( $param_type.minID ) != "":
+      --minSpotId $minID
+    #if str( $param_type.maxID ) != "":
+      --minSpotId $maxID
+    #if str( $param_type.minlen ) != "":
+      --minReadLen $minlen
+    #if str( $param_type.readfilter ) != "":
+      --read-filter $readfilter
+    #if str( $param_type.region ) != "":
+      --aligned-region $region
+    #if $input.input_select=="file":
+      $input.file
+    #else:
+        $input.accession 
+    #end if
+    > $output
   </command>
   <version_string>fastq-dump --version</version_string>
   <inputs>
@@ -21,6 +41,9 @@
 	<param format="text" name="accession" type="text" label="accession"/>
       </when>
     </conditional>
+    <param format="text" name="minID" type="text" label="Minimum spot ID"/>
+    <param format="text" name="maxID" type="text" label="Maximum spot ID"/>
+    <param format="text" name="minlen" type="text" label="Minimum read length"/>
     <param format="text" name="split" type="select" value="">
       <label>Split read pairs</label>
       <option value="">No</option>
@@ -32,6 +55,15 @@
       <option value="--aligned">Only aligned</option>
       <option value="--unaligned">Only unaligned</option>
     </param>
+    <param format="text" name="region" type="text" label="Aligned region"/>
+    <param format="text" name="readfilter" type="select" value="">
+      <label>Filter by value</label>
+      <option value="">None</option>
+      <option value="pass">pass</option>
+      <option value="reject">reject</option>
+      <option value="criteria">criteria</option>
+      <option value="redacted">redacted</option>
+    </param>
   </inputs>
   <outputs>
     <data format="fastqsanger" name="output"/>
diff -r 9ad900168ded -r 7803126704c6 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Jun 30 16:18:09 2013 -0400
+++ b/tool_dependencies.xml	Sun Jun 30 19:20:38 2013 -0400
@@ -23,7 +23,7 @@
   make
   gcc, g++
   libxml2
-  libcurl
+  libcurl4
   zlib
     </readme>
   </package>