# HG changeset patch
# User devteam
# Date 1380121466 14400
# Node ID 04614cf6ed399f2af2e27fe0e5d65d1f4117be00

Uploaded tool tarball.

diff -r 000000000000 -r 04614cf6ed39 fastq_to_fasta.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_to_fasta.xml	Wed Sep 25 11:04:26 2013 -0400
@@ -0,0 +1,82 @@
+<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA">
+	<description>converter</description>
+    <requirements>
+        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
+    </requirements>
+	<command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v 
+#if $input.ext == "fastqsanger":
+-Q 33
+#end if
+	</command>
+
+	<inputs>
+		<param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" />
+
+		<param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
+			<option value="">yes</option>
+			<option value="-n">no</option>
+		</param>
+
+		<param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
+			<option value="-r">yes</option>
+			<option value="">no</option>
+		</param>
+
+	</inputs>
+
+	<tests>
+		<test>
+			<!-- FASTQ-To-FASTA, keep N, don't rename -->
+			<param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
+			<param name="SKIPN" value=""/>
+			<param name="RENAMESEQ" value=""/>
+			<output name="output" file="fastq_to_fasta1a.out" />
+		</test>
+		<test>
+			<!-- FASTQ-To-FASTA, discard N, rename -->
+			<param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
+			<param name="SKIPN" value="no"/>
+			<param name="RENAMESEQ" value="yes"/>
+			<output name="output" file="fastq_to_fasta1b.out" />
+		</test>
+	</tests>
+
+	<outputs>
+		<data format="fasta" name="output" metadata_source="input" />
+	</outputs>
+
+<help>
+
+**What it does**
+
+This tool converts data from Solexa format to FASTA format (scroll down for format description).
+
+--------
+
+**Example**
+
+The following data in Solexa-FASTQ format::
+
+    @CSHL_4_FC042GAMMII_2_1_517_596
+    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+    +CSHL_4_FC042GAMMII_2_1_517_596
+    40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
+  
+Will be converted to FASTA (with 'rename sequence names' = NO)::
+
+    >CSHL_4_FC042GAMMII_2_1_517_596
+    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+    
+Will be converted to FASTA (with 'rename sequence names' = YES)::
+
+    >1
+    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+    
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/    
+</help>
+<!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff -r 000000000000 -r 04614cf6ed39 test-data/fastq_to_fasta1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_to_fasta1.fastq	Wed Sep 25 11:04:26 2013 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
++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
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
++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
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++CSHL_3_FC042AGLLWW:1:2:8:624
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff -r 000000000000 -r 04614cf6ed39 test-data/fastq_to_fasta1a.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_to_fasta1a.out	Wed Sep 25 11:04:26 2013 -0400
@@ -0,0 +1,16 @@
+>CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
+>CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
+>CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
+>CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
+>CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
+>CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
+>CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
+>CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
diff -r 000000000000 -r 04614cf6ed39 test-data/fastq_to_fasta1b.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_to_fasta1b.out	Wed Sep 25 11:04:26 2013 -0400
@@ -0,0 +1,18 @@
+>1
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
+>2
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
+>3
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
+>4
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
+>5
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
+>6
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
+>7
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
+>8
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
+>9
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
diff -r 000000000000 -r 04614cf6ed39 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 25 11:04:26 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>