# HG changeset patch
# User devteam
# Date 1390832798 18000
# Node ID b89bdf6acb6cfc327856b4df86504b292dcc8115

Imported from capsule None

diff -r 000000000000 -r b89bdf6acb6c fastq_paired_end_interlacer.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_paired_end_interlacer.py	Mon Jan 27 09:26:38 2014 -0500
@@ -0,0 +1,59 @@
+#Florent Angly
+import sys
+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner
+
+def main():
+    mate1_filename   = sys.argv[1]
+    mate1_type       = sys.argv[2] or 'sanger'
+    mate2_filename   = sys.argv[3]
+    mate2_type       = sys.argv[4] or 'sanger'
+    outfile_pairs    = sys.argv[5]
+    outfile_singles = sys.argv[6]
+
+    if mate1_type != mate2_type:
+        print "WARNING: You are trying to interlace files of two different types: %s and %s." % ( mate1_type, mate2_type )
+        return
+
+    type = mate1_type
+    joiner = fastqJoiner( type )
+    out_pairs = fastqWriter( open( outfile_pairs, 'wb' ), format = type )
+    out_singles = fastqWriter( open( outfile_singles, 'wb' ), format = type )
+
+    # Pairs + singles present in mate1
+    nof_singles = 0
+    nof_pairs   = 0
+    mate2_input = fastqNamedReader( open( mate2_filename, 'rb' ), format = type )
+    i = None
+    for i, mate1 in enumerate( fastqReader( open( mate1_filename, 'rb' ), format = type ) ):
+        mate2 = mate2_input.get( joiner.get_paired_identifier( mate1 ) )
+        if mate2:
+            out_pairs.write( mate1 )
+            out_pairs.write( mate2 )
+            nof_pairs += 1
+        else:
+            out_singles.write( mate1 )
+            nof_singles += 1
+
+    # Singles present in mate2
+    mate1_input = fastqNamedReader( open( mate1_filename, 'rb' ), format = type )
+    j = None
+    for j, mate2 in enumerate( fastqReader( open( mate2_filename, 'rb' ), format = type ) ):
+        mate1 = mate1_input.get( joiner.get_paired_identifier( mate2 ) )
+        if not mate1:
+            out_singles.write( mate2 )
+            nof_singles += 1
+
+    if (i is None) and (j is None):
+        print "Your input files contained no valid FASTQ sequences."
+    else:
+        print 'There were %s single reads.' % ( nof_singles )
+        print 'Interlaced %s pairs of sequences.' % ( nof_pairs )
+
+    mate1_input.close()
+    mate2_input.close()
+    out_pairs.close()
+    out_singles.close()
+
+ 
+if __name__ == "__main__":
+    main()
diff -r 000000000000 -r b89bdf6acb6c fastq_paired_end_interlacer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_paired_end_interlacer.xml	Mon Jan 27 09:26:38 2014 -0500
@@ -0,0 +1,75 @@
+<tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.1">
+  <description>on paired end reads</description>
+  <requirements>
+    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
+  </requirements>
+  <command interpreter="python">fastq_paired_end_interlacer.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$outfile_pairs' '$outfile_singles'</command>
+  <inputs>
+    <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand mates" />
+    <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand mates" />
+  </inputs>
+  <outputs>
+    <!-- $input1_file.name = filename  , e.g. paired_end_2_errors.fastqsanger -->
+    <!-- $input1_file.id   = ID        , e.g. 10 -->
+    <!-- $input1_file.hid  = history ID, e.g. 5  -->
+    <data name="outfile_pairs"   format="input" label="FASTQ interlacer pairs from data ${input1_file.hid} and data ${input2_file.hid}"/>
+    <data name="outfile_singles" format="input" label="FASTQ interlacer singles from data ${input1_file.hid} and data ${input2_file.hid}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
+      <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
+      <output name="outfile_pairs" file="paired_end_merged.fastqsanger" />
+      <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" />
+    </test>
+    <test>
+      <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />
+      <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />
+      <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" />
+      <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" />
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+This tool joins paired end FASTQ reads from two separate files, one with the left mates and one with the right mates, into a single files where left mates alternate with their right mates. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is included in a separate file.
+
+Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user.
+
+-----
+
+**Input**
+
+Left-hand mates, for example::
+
+    @1539:931/1
+    ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
+    +1539:931/1
+    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+Right-hand mates, for example::
+
+    @1539:931/2
+    CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
+    +1539:931/2
+    WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+-----
+
+**Output**
+
+A multiple-fastq file containing interlaced left and right paired reads::
+
+    @1539:931/1
+    ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
+    +1539:931/1
+    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+    @1539:931/2
+    CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
+    +1539:931/2
+    WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+A multiple-fastq file containing reads that have no mate is also produced.
+
+  </help>
+</tool>
diff -r 000000000000 -r b89bdf6acb6c test-data/paired_end_1.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_end_1.fastqsanger	Mon Jan 27 09:26:38 2014 -0500
@@ -0,0 +1,20 @@
+@1539:931/1
+NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
++1539:931/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@2971:937/1
+NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG
++2971:937/1
+BMQMMRRRSS__________XXXXXVVVVV_b___Y[Y[YXVRVWWPWVX_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@3786:949/1
+NTACCGCGCAACGGCATGATGGCTTGGAACTCACGGTCACGCGCCTGTTTGGCAGAGCCGCCCGCCGAGTCACCTTCCACTAGGAACAGTTCGGAGCGGTT
++3786:949/1
+BKGGKKJNJJ_______W__Y__W_TVPVP[YY[[_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4205:944/1
+NGATCTGGGCTTCAGCAAGACCGATGTCGGCGTGATTGCCAAGCATGCCGGACTCTGGCCGGCGGGGTTCGGCGGTGTGCTGGGTGGCTTGGGGGTGGGGG
++4205:944/1
+BLLLLTWTTR_V_______TYYYRYYYYYY____VWRWWW___BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4534:934/1
+NAATGCCGGTATTTGGCACGATGGCGGCACGCTTCCACGACGACGGGGTGACCTCTCTCTATCAGGCGATGGCATCCAAATTGCACGCGCGGGGTTTGAGG
++4534:934/1
+BGGFGLJLJL______________V____________________YYYPQOTWVT__________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff -r 000000000000 -r b89bdf6acb6c test-data/paired_end_1_errors.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_end_1_errors.fastqsanger	Mon Jan 27 09:26:38 2014 -0500
@@ -0,0 +1,20 @@
+@1539:931/1
+NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
++1539:931/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@2971:937/1
+NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG
++2971:937/1
+BMQMMRRRSS__________XXXXXVVVVV_b___Y[Y[YXVRVWWPWVX_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@3786:949/1
+NTACCGCGCAACGGCATGATGGCTTGGAACTCACGGTCACGCGCCTGTTTGGCAGAGCCGCCCGCCGAGTCACCTTCCACTAGGAACAGTTCGGAGCGGTT
++3786:949/1
+BKGGKKJNJJ_______W__Y__W_TVPVP[YY[[_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@9999:944/1
+NGATCTGGGCTTCAGCAAGACCGATGTCGGCGTGATTGCCAAGCATGCCGGACTCTGGCCGGCGGGGTTCGGCGGTGTGCTGGGTGGCTTGGGGGTGGGGG
++9999:944/1
+BLLLLTWTTR_V_______TYYYRYYYYYY____VWRWWW___BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4534:934/1
+NAATGCCGGTATTTGGCACGATGGCGGCACGCTTCCACGACGACGGGGTGACCTCTCTCTATCAGGCGATGGCATCCAAATTGCACGCGCGGGGTTTGAGG
++4534:934/1
+BGGFGLJLJL______________V____________________YYYPQOTWVT__________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff -r 000000000000 -r b89bdf6acb6c test-data/paired_end_2.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_end_2.fastqsanger	Mon Jan 27 09:26:38 2014 -0500
@@ -0,0 +1,20 @@
+@1539:931/2 this read has a description
+GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
++1539:931/2 this read has a description
+aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@2971:937/2
+CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT
++2971:937/2
+hhhddhefhh_ffffhhhhfah_hhdUdcfW`fbbhfcaec_dfdbba````W^caaaJXGKXSUVYVZY^WY^BBBBBBBBBBBBBBBBBBBBBBBBBBB
+@3786:949/2
+CTCAACCAGAACACCGTGATCGGCGACCAGTTGGCGCAGTTCGCCATCAGAAATGCAGGGATGCGGATGCGGGCTAGCACGAAAGTCATCCTCAACACGAT
++3786:949/2
+ffcfcaffff\_edefddff[ffa_fRffRdc]Sdf]affehh_eaebBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4205:944/2
+GTCGACAGGTGCCTGTACACCACGCCAGGCCAGCCAGGCGAAACCGAGAACGGTCACCATCTGAACCAGACCGAAAACCAACAGTGCGGGGTTGAGCCACG
++4205:944/2
+hhhhhcffcWcdfdcffdffdfQadf[fLfc`Ra`Wcca]`^``]L[^QZGSQWUYZXK[`bJRbZb[_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4534:934/2
+GGTAATTGCGGACGGCTTCGGCAATTTCGGCCAGGTAGCGCACGCGCTTCGACGGAACGATGGCGCGCAGGTTCGACGATTGTCGAACGCTGATCAGCGCG
++4534:934/2
+ffffcff[fdhaghh[ffcahhghhhdhadhhhhg_hc[hf]fec]faa]bLb___`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff -r 000000000000 -r b89bdf6acb6c test-data/paired_end_2_errors.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_end_2_errors.fastqsanger	Mon Jan 27 09:26:38 2014 -0500
@@ -0,0 +1,20 @@
+@1539:931/2
+GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
++1539:931/2
+aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@2971:937/2
+CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT
++2971:937/2
+hhhddhefhh_ffffhhhhfah_hhdUdcfW`fbbhfcaec_dfdbba````W^caaaJXGKXSUVYVZY^WY^BBBBBBBBBBBBBBBBBBBBBBBBBBB
+@9999:949/2
+CTCAACCAGAACACCGTGATCGGCGACCAGTTGGCGCAGTTCGCCATCAGAAATGCAGGGATGCGGATGCGGGCTAGCACGAAAGTCATCCTCAACACGAT
++9999:949/2
+ffcfcaffff\_edefddff[ffa_fRffRdc]Sdf]affehh_eaebBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4205:944/2
+GTCGACAGGTGCCTGTACACCACGCCAGGCCAGCCAGGCGAAACCGAGAACGGTCACCATCTGAACCAGACCGAAAACCAACAGTGCGGGGTTGAGCCACG
++4205:944/2
+hhhhhcffcWcdfdcffdffdfQadf[fLfc`Ra`Wcca]`^``]L[^QZGSQWUYZXK[`bJRbZb[_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4534:934/2
+GGTAATTGCGGACGGCTTCGGCAATTTCGGCCAGGTAGCGCACGCGCTTCGACGGAACGATGGCGCGCAGGTTCGACGATTGTCGAACGCTGATCAGCGCG
++4534:934/2
+ffffcff[fdhaghh[ffcahhghhhdhadhhhhg_hc[hf]fec]faa]bLb___`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff -r 000000000000 -r b89bdf6acb6c test-data/paired_end_merged.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_end_merged.fastqsanger	Mon Jan 27 09:26:38 2014 -0500
@@ -0,0 +1,40 @@
+@1539:931/1
+NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
++1539:931/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@1539:931/2 this read has a description
+GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
++1539:931/2 this read has a description
+aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@2971:937/1
+NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG
++2971:937/1
+BMQMMRRRSS__________XXXXXVVVVV_b___Y[Y[YXVRVWWPWVX_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@2971:937/2
+CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT
++2971:937/2
+hhhddhefhh_ffffhhhhfah_hhdUdcfW`fbbhfcaec_dfdbba````W^caaaJXGKXSUVYVZY^WY^BBBBBBBBBBBBBBBBBBBBBBBBBBB
+@3786:949/1
+NTACCGCGCAACGGCATGATGGCTTGGAACTCACGGTCACGCGCCTGTTTGGCAGAGCCGCCCGCCGAGTCACCTTCCACTAGGAACAGTTCGGAGCGGTT
++3786:949/1
+BKGGKKJNJJ_______W__Y__W_TVPVP[YY[[_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@3786:949/2
+CTCAACCAGAACACCGTGATCGGCGACCAGTTGGCGCAGTTCGCCATCAGAAATGCAGGGATGCGGATGCGGGCTAGCACGAAAGTCATCCTCAACACGAT
++3786:949/2
+ffcfcaffff\_edefddff[ffa_fRffRdc]Sdf]affehh_eaebBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4205:944/1
+NGATCTGGGCTTCAGCAAGACCGATGTCGGCGTGATTGCCAAGCATGCCGGACTCTGGCCGGCGGGGTTCGGCGGTGTGCTGGGTGGCTTGGGGGTGGGGG
++4205:944/1
+BLLLLTWTTR_V_______TYYYRYYYYYY____VWRWWW___BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4205:944/2
+GTCGACAGGTGCCTGTACACCACGCCAGGCCAGCCAGGCGAAACCGAGAACGGTCACCATCTGAACCAGACCGAAAACCAACAGTGCGGGGTTGAGCCACG
++4205:944/2
+hhhhhcffcWcdfdcffdffdfQadf[fLfc`Ra`Wcca]`^``]L[^QZGSQWUYZXK[`bJRbZb[_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4534:934/1
+NAATGCCGGTATTTGGCACGATGGCGGCACGCTTCCACGACGACGGGGTGACCTCTCTCTATCAGGCGATGGCATCCAAATTGCACGCGCGGGGTTTGAGG
++4534:934/1
+BGGFGLJLJL______________V____________________YYYPQOTWVT__________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4534:934/2
+GGTAATTGCGGACGGCTTCGGCAATTTCGGCCAGGTAGCGCACGCGCTTCGACGGAACGATGGCGCGCAGGTTCGACGATTGTCGAACGCTGATCAGCGCG
++4534:934/2
+ffffcff[fdhaghh[ffcahhghhhdhadhhhhg_hc[hf]fec]faa]bLb___`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff -r 000000000000 -r b89bdf6acb6c test-data/paired_end_merged_cleaned.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_end_merged_cleaned.fastqsanger	Mon Jan 27 09:26:38 2014 -0500
@@ -0,0 +1,24 @@
+@1539:931/1
+NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
++1539:931/1
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@1539:931/2
+GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
++1539:931/2
+aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@2971:937/1
+NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG
++2971:937/1
+BMQMMRRRSS__________XXXXXVVVVV_b___Y[Y[YXVRVWWPWVX_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@2971:937/2
+CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT
++2971:937/2
+hhhddhefhh_ffffhhhhfah_hhdUdcfW`fbbhfcaec_dfdbba````W^caaaJXGKXSUVYVZY^WY^BBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4534:934/1
+NAATGCCGGTATTTGGCACGATGGCGGCACGCTTCCACGACGACGGGGTGACCTCTCTCTATCAGGCGATGGCATCCAAATTGCACGCGCGGGGTTTGAGG
++4534:934/1
+BGGFGLJLJL______________V____________________YYYPQOTWVT__________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4534:934/2
+GGTAATTGCGGACGGCTTCGGCAATTTCGGCCAGGTAGCGCACGCGCTTCGACGGAACGATGGCGCGCAGGTTCGACGATTGTCGAACGCTGATCAGCGCG
++4534:934/2
+ffffcff[fdhaghh[ffcahhghhhdhadhhhhg_hc[hf]fec]faa]bLb___`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff -r 000000000000 -r b89bdf6acb6c test-data/paired_end_merged_cleaned_singles.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_end_merged_cleaned_singles.fastqsanger	Mon Jan 27 09:26:38 2014 -0500
@@ -0,0 +1,16 @@
+@3786:949/1
+NTACCGCGCAACGGCATGATGGCTTGGAACTCACGGTCACGCGCCTGTTTGGCAGAGCCGCCCGCCGAGTCACCTTCCACTAGGAACAGTTCGGAGCGGTT
++3786:949/1
+BKGGKKJNJJ_______W__Y__W_TVPVP[YY[[_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@9999:944/1
+NGATCTGGGCTTCAGCAAGACCGATGTCGGCGTGATTGCCAAGCATGCCGGACTCTGGCCGGCGGGGTTCGGCGGTGTGCTGGGTGGCTTGGGGGTGGGGG
++9999:944/1
+BLLLLTWTTR_V_______TYYYRYYYYYY____VWRWWW___BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@9999:949/2
+CTCAACCAGAACACCGTGATCGGCGACCAGTTGGCGCAGTTCGCCATCAGAAATGCAGGGATGCGGATGCGGGCTAGCACGAAAGTCATCCTCAACACGAT
++9999:949/2
+ffcfcaffff\_edefddff[ffa_fRffRdc]Sdf]affehh_eaebBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@4205:944/2
+GTCGACAGGTGCCTGTACACCACGCCAGGCCAGCCAGGCGAAACCGAGAACGGTCACCATCTGAACCAGACCGAAAACCAACAGTGCGGGGTTGAGCCACG
++4205:944/2
+hhhhhcffcWcdfdcffdffdfQadf[fLfc`Ra`Wcca]`^``]L[^QZGSQWUYZXK[`bJRbZb[_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
diff -r 000000000000 -r b89bdf6acb6c test-data/paired_end_merged_singles.fastqsanger
diff -r 000000000000 -r b89bdf6acb6c tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jan 27 09:26:38 2014 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="galaxy_sequence_utils" version="1.0.0">
+      <repository changeset_revision="0643676ad5f7" name="package_galaxy_utils_1_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>