# HG changeset patch
# User devteam
# Date 1380122487 14400
# Node ID 9cb372481a71ffe763a7538542b15dc3b79ea7cf
Uploaded tool tarball.
diff -r 000000000000 -r 9cb372481a71 fastx_trimmer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_trimmer.xml Wed Sep 25 11:21:27 2013 -0400
@@ -0,0 +1,83 @@
+
+
+
+ fastx_toolkit
+
+ zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This tool trims (cut bases from) sequences in a FASTA/Q file.
+
+--------
+
+**Example**
+
+Input Fasta file (with 36 bases in each sequences)::
+
+ >1-1
+ TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
+ >2-1
+ CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
+
+
+Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
+
+ >1-1
+ TATGGTCAGAAACCATATGCA
+ >2-1
+ CAGCGAGGCTTTAATGCCATT
+
+Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
+
+ >1-1
+ TCAGA
+ >2-1
+ AGGCT
+
+ ------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+
+
+
+
diff -r 000000000000 -r 9cb372481a71 test-data/fastx_trimmer1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_trimmer1.fasta Wed Sep 25 11:21:27 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 9cb372481a71 test-data/fastx_trimmer1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_trimmer1.out Wed Sep 25 11:21:27 2013 -0400
@@ -0,0 +1,4 @@
+>CSHL__2_FC042NGABCD:8:1:120:202
+TAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+>CSHL__2_FC042NGABCD:8:1:103:1185
+CGATAGATCGGCAGAGCTCGTTTACCGTCTTC
diff -r 000000000000 -r 9cb372481a71 test-data/fastx_trimmer2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_trimmer2.fastq Wed Sep 25 11:21:27 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 9cb372481a71 test-data/fastx_trimmer2.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_trimmer2.out Wed Sep 25 11:21:27 2013 -0400
@@ -0,0 +1,8 @@
+@CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCC
++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
+@CSHL__2_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTT
++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
diff -r 000000000000 -r 9cb372481a71 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Sep 25 11:21:27 2013 -0400
@@ -0,0 +1,6 @@
+
+
+
+
+
+