# HG changeset patch
# User devteam
# Date 1380121198 14400
# Node ID b87c74b61d81901271f3a6407fae182131af9eb9

Uploaded tool tarball.

diff -r 000000000000 -r b87c74b61d81 fastq_quality_converter.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_quality_converter.xml	Wed Sep 25 10:59:58 2013 -0400
@@ -0,0 +1,99 @@
+<tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.0">
+	<description>(ASCII-Numeric)</description>
+    <requirements>
+        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
+    </requirements>
+	<command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output -Q $offset</command>
+	<inputs>
+		<param format="fastq" name="input" type="data" label="Library to convert" />
+
+		<param name="QUAL_FORMAT" type="select" label="Desired output format">
+			<option value="-a">ASCII (letters) quality scores</option>
+			<option value="-n">Numeric quality scores</option>
+		</param>
+		
+        <param name="offset" type="select" label="FASTQ ASCII offset">
+            <option value="33">33</option>
+            <option selected="true" value="64">64</option>
+        </param>	
+    </inputs>
+
+	<tests>
+		<test>
+			<!-- ASCII to NUMERIC -->
+			<param name="input" value="fastq_qual_conv1.fastq" />
+			<param name="QUAL_FORMAT" value="Numeric quality scores" />
+			<param name="offset" value="64" />
+			<output name="output" file="fastq_qual_conv1.out" />
+		</test>
+		<test>
+			<!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output -->
+			<param name="input" value="fastq_qual_conv1.fastq" />
+			<param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
+			<param name="offset" value="64" />
+			<output name="output" file="fastq_qual_conv1a.out" />
+		</test>
+		<test>
+			<!-- NUMERIC to ASCII -->
+			<param name="input" value="fastq_qual_conv2.fastq" />
+			<param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
+			<param name="offset" value="64" />
+			<output name="output" file="fastq_qual_conv2.out" />
+		</test>
+		<test>
+			<!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output -->
+			<param name="input" value="fastq_qual_conv2.fastq" />
+			<param name="QUAL_FORMAT" value="Numeric quality scores" />
+			<param name="offset" value="64" />
+			<output name="output" file="fastq_qual_conv2n.out" />
+		</test>
+	</tests>
+
+	<outputs>
+		<data format="fastq" name="output" metadata_source="input" />
+	</outputs>
+<help>
+
+**What it does**
+
+Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
+
+.. class:: warningmark 
+
+Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale).
+
+
+-----
+
+FASTQ with Numeric quality scores::
+
+    @CSHL__2_FC042AGWWWXX:8:1:120:202
+    ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+    +CSHL__2_FC042AGWWWXX:8:1:120:202
+    40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8
+    @CSHL__2_FC042AGWWWXX:8:1:103:1185
+    ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
+    +CSHL__2_FC042AGWWWXX:8:1:103:1185
+    40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2
+
+
+FASTQ with ASCII quality scores::
+
+    @CSHL__2_FC042AGWWWXX:8:1:120:202
+    ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+    +CSHL__2_FC042AGWWWXX:8:1:120:202
+    hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH
+    @CSHL__2_FC042AGWWWXX:8:1:103:1185
+    ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
+    +CSHL__2_FC042AGWWWXX:8:1:103:1185
+    hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+ 
+</help>
+<!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff -r 000000000000 -r b87c74b61d81 test-data/fastq_qual_conv1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_qual_conv1.fastq	Wed Sep 25 10:59:58 2013 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC
++CSHL_3_FC042AGLLWW:1:2:7:33
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACACACACTCATCGTCGTCCCCCG
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACCC
++CSHL_3_FC042AGLLWW:1:2:7:1819
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:8:624
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff -r 000000000000 -r b87c74b61d81 test-data/fastq_qual_conv1.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_qual_conv1.out	Wed Sep 25 10:59:58 2013 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+33 33 34 30 22 30 33 21 29 32 33 33 30 33 26 33 33 33 34 34 24 5 26 33 34 33 33 33 33 33 33 33 33 29 29 32
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC
++CSHL_3_FC042AGLLWW:1:2:7:33
+23 33 33 33 30 33 26 33 33 23 30 21 31 24 33 23 33 33 28 23 13 5 16 30 11 5 26 24 18 16 5 5 5 7 33 33
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+33 31 13 30 33 28 21 33 33 33 31 13 31 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 22 28 26 21 7 21 21 18
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+33 30 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 31 21 32 33 33 33 33 33 31 19 31 33 33 33 33 33 22 22 27
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACACACACTCATCGTCGTCCCCCG
++CSHL_3_FC042AGLLWW:1:2:7:292
+34 33 34 33 33 33 33 33 33 33 21 13 33 33 33 33 33 33 33 33 33 33 33 28 24 5 21 21 5 16 31 29 21 5 18 5
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACCC
++CSHL_3_FC042AGLLWW:1:2:7:1819
+33 28 28 17 22 22 22 12 33 33 12 15 5 24 21 23 21 21 5 11 21 21 12 5 13 21 5 21 21 11 21 12 9 17 13 21
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+33 33 33 33 33 33 33 33 33 24 21 24 24 5 24 33 33 33 33 33 32 31 26 33 33 33 33 33 33 33 33 33 24 5 24 21
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:8:624
+33 33 27 19 30 32 24 32 33 33 31 29 29 15 15 24 13 21 30 31 27 13 21 31 33 33 33 33 33 33 33 33 33 33 33 33
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT
++CSHL_3_FC042AGLLWW:1:2:8:250
+33 33 33 33 33 33 33 33 30 33 33 33 33 33 33 34 34 34 27 11 24 16 5 21 27 18 24 26 30 10 21 11 18 11 24 5
diff -r 000000000000 -r b87c74b61d81 test-data/fastq_qual_conv1a.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_qual_conv1a.out	Wed Sep 25 10:59:58 2013 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC
++CSHL_3_FC042AGLLWW:1:2:7:33
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACACACACTCATCGTCGTCCCCCG
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACCC
++CSHL_3_FC042AGLLWW:1:2:7:1819
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:8:624
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff -r 000000000000 -r b87c74b61d81 test-data/fastq_qual_conv2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_qual_conv2.fastq	Wed Sep 25 10:59:58 2013 -0400
@@ -0,0 +1,60 @@
+@CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:233:1674
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30
+@CSHL_3_FC0420AGLLKK:2:1:136:448
+GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA
++CSHL_3_FC0420AGLLKK:2:1:136:448
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10
+@CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:237:1037
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11
+@CSHL_3_FC0420AGLLKK:2:1:1601:1525
+AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1601:1525
+40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14
+@CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1805:1464
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10
+@CSHL_3_FC0420AGLLKK:2:1:1713:528
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1713:528
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11
+@CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
++CSHL_3_FC0420AGLLKK:2:1:126:1087
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22
+@CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1488:1323
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9
+@CSHL_3_FC0420AGLLKK:2:1:913:199
+GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:913:199
+40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21
+@CSHL_3_FC0420AGLLKK:2:1:1236:1157
+AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1236:1157
+40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19
+@CSHL_3_FC0420AGLLKK:2:1:928:765
+GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC
++CSHL_3_FC0420AGLLKK:2:1:928:765
+40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11
+@CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
++CSHL_3_FC0420AGLLKK:2:1:727:1020
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18
+@CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:758:1799
+40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11
+@CSHL_3_FC0420AGLLKK:2:1:1818:550
+AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1818:550
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18
+@CSHL_3_FC0420AGLLKK:2:1:1764:391
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC0420AGLLKK:2:1:1764:391
+40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22
diff -r 000000000000 -r b87c74b61d81 test-data/fastq_qual_conv2.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_qual_conv2.out	Wed Sep 25 10:59:58 2013 -0400
@@ -0,0 +1,60 @@
+@CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:233:1674
+hhhhhhhhhhhhhhhhhh`hhhhPTYIUehhP]Z^
+@CSHL_3_FC0420AGLLKK:2:1:136:448
+GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA
++CSHL_3_FC0420AGLLKK:2:1:136:448
+hhhhhhhhhhhhhhhhhhhhhhh;MQ\hhHQ[HMJ
+@CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:237:1037
+hhhhhhhhhhhhhhhDhhZchfhFhh@CZ`[NKZK
+@CSHL_3_FC0420AGLLKK:2:1:1601:1525
+AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1601:1525
+hhhhhhhhhhhhchhLhh^^hhhLdWQXRVYOJbN
+@CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1805:1464
+hhhhhhhhhhhhhhhhhPW\hUhIeMTUGKNNFWJ
+@CSHL_3_FC0420AGLLKK:2:1:1713:528
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1713:528
+hhhhhhhhhhhhhhhhhhhhh`hLfOVTQNLJGVK
+@CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
++CSHL_3_FC0420AGLLKK:2:1:126:1087
+hhhhhhhhhhhhhhYhhhhhhh_hhKJWhMLQeQV
+@CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1488:1323
+hhhhhhhhhhhhhhhhhhgV_hhL]V@GLHRGCRI
+@CSHL_3_FC0420AGLLKK:2:1:913:199
+GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:913:199
+hhghhhhhhhhhDhhXbTaUd`h;hMUUZQRYNYU
+@CSHL_3_FC0420AGLLKK:2:1:1236:1157
+AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1236:1157
+hhhhhhhhhhhhhchhhhhahehhhRPTWV_ZJVS
+@CSHL_3_FC0420AGLLKK:2:1:928:765
+GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC
++CSHL_3_FC0420AGLLKK:2:1:928:765
+hhhhhhhhhhhhhY[hec[hhQh;dKSOSPKLLWK
+@CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
++CSHL_3_FC0420AGLLKK:2:1:727:1020
+hhhhhhhhhhhhhhhhhhhhhh^hhXRfaZPWVPR
+@CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:758:1799
+hhhhhhhhchghh[ThQbOhhhhO\QDLJJRNCNK
+@CSHL_3_FC0420AGLLKK:2:1:1818:550
+AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1818:550
+hhhhhhhhhhhhhhd`hahhfeh\][VMTSQQMaR
+@CSHL_3_FC0420AGLLKK:2:1:1764:391
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC0420AGLLKK:2:1:1764:391
+hhhhhhhhhhhahhhhhXhhhhhLhXNIVO]RKhV
diff -r 000000000000 -r b87c74b61d81 test-data/fastq_qual_conv2n.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_qual_conv2n.out	Wed Sep 25 10:59:58 2013 -0400
@@ -0,0 +1,60 @@
+@CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:233:1674
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30
+@CSHL_3_FC0420AGLLKK:2:1:136:448
+GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA
++CSHL_3_FC0420AGLLKK:2:1:136:448
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10
+@CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:237:1037
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11
+@CSHL_3_FC0420AGLLKK:2:1:1601:1525
+AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1601:1525
+40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14
+@CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1805:1464
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10
+@CSHL_3_FC0420AGLLKK:2:1:1713:528
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1713:528
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11
+@CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
++CSHL_3_FC0420AGLLKK:2:1:126:1087
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22
+@CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1488:1323
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9
+@CSHL_3_FC0420AGLLKK:2:1:913:199
+GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:913:199
+40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21
+@CSHL_3_FC0420AGLLKK:2:1:1236:1157
+AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1236:1157
+40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19
+@CSHL_3_FC0420AGLLKK:2:1:928:765
+GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC
++CSHL_3_FC0420AGLLKK:2:1:928:765
+40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11
+@CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
++CSHL_3_FC0420AGLLKK:2:1:727:1020
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18
+@CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:758:1799
+40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11
+@CSHL_3_FC0420AGLLKK:2:1:1818:550
+AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1818:550
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18
+@CSHL_3_FC0420AGLLKK:2:1:1764:391
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC0420AGLLKK:2:1:1764:391
+40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22
diff -r 000000000000 -r b87c74b61d81 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 25 10:59:58 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="fastx_toolkit" version="0.0.13">
+        <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>