# HG changeset patch
# User devteam
# Date 1380122425 14400
# Node ID c58871138668be81a701c785a5e9a050849c0b88
Uploaded tool tarball.
diff -r 000000000000 -r c58871138668 fastx_reverse_complement.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_reverse_complement.xml Wed Sep 25 11:20:25 2013 -0400
@@ -0,0 +1,65 @@
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+ fastx_toolkit
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+ zcat -f '$input' | fastx_reverse_complement -v -o $output
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
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+**What it does**
+
+This tool reverse-complements each sequence in a library.
+If the library is a FASTQ, the quality-scores are also reversed.
+
+--------
+
+**Example**
+
+Input FASTQ file::
+
+ @CSHL_1_FC42AGWWWXX:8:1:3:740
+ TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
+ +CSHL_1_FC42AGWWWXX:8:1:3:740
+ 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
+
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+Output FASTQ file::
+
+ @CSHL_1_FC42AGWWWXX:8:1:3:740
+ TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
+ +CSHL_1_FC42AGWWWXX:8:1:3:740
+ 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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diff -r 000000000000 -r c58871138668 test-data/fastx_rev_comp1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_rev_comp1.fasta Wed Sep 25 11:20:25 2013 -0400
@@ -0,0 +1,4 @@
+>CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+>CSHL__2_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
diff -r 000000000000 -r c58871138668 test-data/fastx_rev_comp2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_rev_comp2.fastq Wed Sep 25 11:20:25 2013 -0400
@@ -0,0 +1,8 @@
+@CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
++CSHL__2_FC042NGABCD: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_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
++CSHL__2_FC042NGABCD: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
diff -r 000000000000 -r c58871138668 test-data/fastx_reverse_complement1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_reverse_complement1.out Wed Sep 25 11:20:25 2013 -0400
@@ -0,0 +1,4 @@
+>CSHL__2_FC042NGABCD:8:1:120:202
+GCAGAAAACGGCATACTAGCTCTTCCGATCTATCGT
+>CSHL__2_FC042NGABCD:8:1:103:1185
+GAAGACGGTAAACGAGCTCTGCCGATCTATCGTGAT
diff -r 000000000000 -r c58871138668 test-data/fastx_reverse_complement2.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_reverse_complement2.out Wed Sep 25 11:20:25 2013 -0400
@@ -0,0 +1,8 @@
+@CSHL__2_FC042NGABCD:8:1:120:202
+GCAGAAAACGGCATACTAGCTCTTCCGATCTATCGT
++CSHL__2_FC042NGABCD:8:1:120:202
+8 10 21 -1 10 11 -1 7 3 1 8 40 27 14 40 30 -1 40 20 40 25 40 40 28 40 40 6 40 40 40 40 20 40 40 40 40
+@CSHL__2_FC042NGABCD:8:1:103:1185
+GAAGACGGTAAACGAGCTCTGCCGATCTATCGTGAT
++CSHL__2_FC042NGABCD:8:1:103:1185
+2 30 25 4 2 8 0 10 3 23 12 22 34 15 36 8 14 17 22 9 0 40 22 30 32 40 40 40 31 33 35 40 40 40 40 40
diff -r 000000000000 -r c58871138668 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Sep 25 11:20:25 2013 -0400
@@ -0,0 +1,6 @@
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