# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1375672673 14400
# Node ID a0925f507352fddaabd15b08c5a4679077e41942
# Parent  4da2d7f0128e25a185b4baea4ddc8e8c6882a55c
bring pileup to parity with sam; fixed minMapq for sam

diff -r 4da2d7f0128e -r a0925f507352 sam_dump.xml
--- a/sam_dump.xml	Thu Aug 01 13:57:27 2013 -0400
+++ b/sam_dump.xml	Sun Aug 04 23:17:53 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Extract reads" version="1.1.0">
+<tool id="sam_dump" name="Extract reads" version="1.1.1">
   <description> in SAM format from NCBI SRA.</description>
   <command>
     sam-dump --log-level fatal 
@@ -8,6 +8,9 @@
     #if str( $matepairDist ) != "":
       --matepair-distance $matepairDist
     #end if
+    #if str( $minMapq ) != "":
+      --minmapq $minMapq
+    #end if
     #if $header == "yes":
       --header
     #else:
diff -r 4da2d7f0128e -r a0925f507352 sra_pileup.xml
--- a/sra_pileup.xml	Thu Aug 01 13:57:27 2013 -0400
+++ b/sra_pileup.xml	Sun Aug 04 23:17:53 2013 -0400
@@ -1,18 +1,42 @@
-<tool id="sra_pileup" name="Generate pileup format" version="1.0.0">
+<tool id="sra_pileup" name="Generate pileup format" version="1.0.1">
   <description> from NCBI sra.</description>
-  <command>sra-pileup '$input' > $output</command>
+  <command>sra-pileup --log-level fatal 
+    #if str( $region ) != "":
+      --aligned-region $region
+    #end if
+    #if str( $minMapq ) != "":
+      --minmapq $minMapq
+    #end if
+    #if $input.input_select == "file":
+      $input.file
+    #else:
+      $input.accession 
+    #end if
+    > $output</command>
   <version_string>sra-pileup --version</version_string>
   <inputs>
-    <param format="sra" name="input" type="data" label="sra archive"/>
+    <conditional name="input">
+      <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>
+      </param>
+      <when value="file">
+    <param format="sra" name="file" type="data" label="sra archive"/>
+      </when>
+      <when value="accession_number">
+    <param format="text" name="accession" type="text" label="accession"/>
+      </when>
+    </conditional>
+    <param format="text" name="region" type="text" label="aligned region"/>
+    <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
   </inputs>
   <outputs>
-    <data format="sam" name="output"/>
+    <data format="pileup" name="output"/>
   </outputs>
   <requirements>
     <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
   </requirements>
   <help>
-    !!! Note that this tool does not function correctly !!!
     This tool produces pileup format from sra archives using sra-pileup. 
     The sra-pileup 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.