# HG changeset patch
# User peterjc
# Date 1415099273 18000
# Node ID 27135d7637b6c9469a00e92f3c54ac45ad6c079d
# Parent  03adf9de156e395bdf0e2c561e3e3b3d817c463f
Uploaded v0.0.1b, now includes -n and -O options.

diff -r 03adf9de156e -r 27135d7637b6 test-data/sam_spec_padded.bam2fq_no_suf.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam_spec_padded.bam2fq_no_suf.fastq	Tue Nov 04 06:07:53 2014 -0500
@@ -0,0 +1,12 @@
+>ref
+AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
+>r001
+TTAGATAAAGGATACTG
+>r002
+AAAAGATAAGGATA
+>r003
+AGCTAA
+>r004
+ATAGCTTCAGC
+>r001
+ATGCCGCTG
diff -r 03adf9de156e -r 27135d7637b6 tools/samtools_bam2fq/README.rst
--- a/tools/samtools_bam2fq/README.rst	Mon Nov 03 11:44:44 2014 -0500
+++ b/tools/samtools_bam2fq/README.rst	Tue Nov 04 06:07:53 2014 -0500
@@ -61,7 +61,7 @@
 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder::
 
-    $ tar -czf samtools_bam2fq.tar.gz tools/samtools_bam2fq/README.rst tools/samtools_bam2fq/samtools_bam2fq.xml tools/samtools_bam2fq/tool_dependencies.xml test-data/sam_spec_padded.bam test-data/sam_spec_padded.sam test-data/sam_spec_padded.depad.bam test-data/sam_spec_padded.bam2fq.fastq
+    $ tar -czf samtools_bam2fq.tar.gz tools/samtools_bam2fq/README.rst tools/samtools_bam2fq/samtools_bam2fq.xml tools/samtools_bam2fq/tool_dependencies.xml test-data/sam_spec_padded.bam test-data/sam_spec_padded.sam test-data/sam_spec_padded.depad.bam test-data/sam_spec_padded.bam2fq.fastq test-data/sam_spec_padded.bam2fq_no_suf.fastq
 
 Check this worked::
 
@@ -73,6 +73,7 @@
     test-data/sam_spec_padded.sam
     test-data/sam_spec_padded.depad.bam
     test-data/sam_spec_padded.bam2fq.fastq
+    test-data/sam_spec_padded.bam2fq_no_suf.fastq
 
 
 Licence (MIT)
diff -r 03adf9de156e -r 27135d7637b6 tools/samtools_bam2fq/samtools_bam2fq.xml
--- a/tools/samtools_bam2fq/samtools_bam2fq.xml	Mon Nov 03 11:44:44 2014 -0500
+++ b/tools/samtools_bam2fq/samtools_bam2fq.xml	Tue Nov 04 06:07:53 2014 -0500
@@ -5,11 +5,15 @@
         <requirement type="package" version="1.1">samtools</requirement>
     </requirements>
     <version_command>samtools 2&gt;&amp;1 | grep -i "Version:"</version_command>
-    <command>samtools bam2fq "$input_bam" &gt; "$out_fastq"</command>
+    <command>samtools bam2fq $suffices $orig_qual "$input_bam" &gt; "$out_fastq"</command>
     <inputs>
         <!-- Unlike other bits of samtools, this seems to autodetect SAM vs BAM -->
         <param name="input_bam" type="data" format="bam,sam" label="Input BAM file" />
-	<!-- TODO - new options -n, -O and -s in samtools v1.1 -->
+        <param name="suffices" type="boolean" label="Add /1 and /2 suffices to paired reads?"
+	       truevalue="" falsevalue="-n" checked="true" />
+        <param name="orig_qual" type="boolean" label="Use original qualities (OQ tags) if present?"
+               truevalue="-O" falsevalue="" checked="false" />
+	<!-- TODO - new option -s in samtools v1.1 -->
     </inputs>
     <outputs>
         <data name="out_fastq" format="fastqsanger" label="$input_bam.name (bam2fq)" />
@@ -22,6 +26,14 @@
     <tests>
         <test>
             <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
+            <param name="suffices" value="true" />
+            <param name="orig_qual" value="false" />
+            <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
+            <param name="suffices" value="true" />
+            <param name="orig_qual" value="true" />
             <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" />
         </test>
         <test>
@@ -32,6 +44,11 @@
             <param name="input_bam" value="sam_spec_padded.depad.bam" ftype="bam" />
             <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" />
         </test>
+        <test>
+            <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
+            <param name="suffices" value="false"/>
+            <output name="out_fastq" file="sam_spec_padded.bam2fq_no_suf.fastq" ftype="fastqsanger" />
+        </test>
     </tests>
     <help>
 **What it does**