Mercurial > repos > devteam > fastq_quality_converter
changeset 0:b87c74b61d81 draft
Uploaded tool tarball.
| author | devteam |
|---|---|
| date | Wed, 25 Sep 2013 10:59:58 -0400 |
| parents | |
| children | 74db4cffab1f |
| files | fastq_quality_converter.xml test-data/fastq_qual_conv1.fastq test-data/fastq_qual_conv1.out test-data/fastq_qual_conv1a.out test-data/fastq_qual_conv2.fastq test-data/fastq_qual_conv2.out test-data/fastq_qual_conv2n.out tool_dependencies.xml |
| diffstat | 8 files changed, 393 insertions(+), 0 deletions(-) [+] |
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--- /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>
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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>