diff sam_dump.xml @ 37:4da2d7f0128e draft

Exposed more options for fastq_dump and sam_dump

--- a/sam_dump.xml	Sun Jun 30 19:50:44 2013 -0400
+++ b/sam_dump.xml	Thu Aug 01 13:57:27 2013 -0400
@@ -1,24 +1,67 @@
-<tool id="sam_dump" name="Extract SAM" version="1.0.2">
-  <description> format reads from NCBI sra.</description>
-  <command>sam-dump $header $aligned $primary '$input' > $output</command>
+<tool id="sam_dump" name="Extract reads" version="1.1.0">
+  <description> in SAM format from NCBI SRA.</description>
+  <command>
+    sam-dump --log-level fatal 
+    #if str( $region ) != "":
+      --aligned-region $region
+    #end if
+    #if str( $matepairDist ) != "":
+      --matepair-distance $matepairDist
+    #end if
+    #if $header == "yes":
+      --header
+    #else:
+      --no-header 
+    #end if
+    #if str( $alignments ) == "both":
+      --unaligned
+    #end if
+    #if str( $alignments ) == "unaligned":
+      --unaligned-spots-only
+    #end if
+    #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ):
+      --primary
+    #end if
+    #if $input.input_select == "file":
+      $input.file
+    #else:
+      $input.accession 
+    #end if
+    > $output
+  </command>  
   <version_string>sam-dump --version</version_string>
   <inputs>
-    <param format="SRA" name="input" type="data" label="sra archive"/>
-    <param format="text" name="header" type="select" value="">
-      <label>Output SAM header</label>
-      <option value="--header">Yes</option>
-      <option value="--no-header">No</option>
+    <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="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/>
+    <param format="text" name="header" type="select" value="yes">
+      <label>output SAM header</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
     </param>
-    <param format="text" name="aligned" type="select" value="">
-      <label>Output unaligned reads as well as aligned reads</label>
-      <option value="">No</option>
-      <option value="--unaligned">Yes</option>
+    <param format="text" name="alignments" type="select" value="both">
+      <label>aligned or unaligned reads</label>
+      <option value="both">both</option>
+      <option value="aligned">aligned only</option>
+        <option value="unaligned">unaligned only</option>
     </param>
-    <param format="text" name="primary" type="select" value="">
-      <label>Output only primary aligments</label>
-      <option value="">No</option>
-      <option value="--primary">Yes</option>
+    <param format="text" name="primary" type="select" value="no">
+      <label>only primary aligments</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
     </param>
+    <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
   </inputs>
   <outputs>
     <data format="sam" name="output"/>
@@ -27,8 +70,8 @@
     <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
   </requirements>
   <help>
-    This tool extracts sam format reads from sra archives using sam-dump. 
+    This tool extracts reads from sra archives using sam-dump. 
     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 [e-mail] for support and bug reports.
   </help>
-</tool>
+</tool>
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