# HG changeset patch
# User devteam
# Date 1380121003 14400
# Node ID 4b41e3076a50dd3c1f1e3cf03843e3cc199a465d

Uploaded tool tarball.

diff -r 000000000000 -r 4b41e3076a50 fasta_nucleotide_changer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_nucleotide_changer.xml	Wed Sep 25 10:56:43 2013 -0400
@@ -0,0 +1,75 @@
+<tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" >
+	<description>converter</description>
+    <requirements>
+        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
+    </requirements>
+	<command>zcat -f '$input' | fasta_nucleotide_changer -$mode -v -o $output</command>
+	<inputs>
+		<param format="fasta" version="1.0.0" name="input" type="data" label="Library to convert" />
+
+		<param version="1.0.0" name="mode" type="select" label="Convert">
+			<option value="d">RNA to DNA (U to T)</option>
+			<option value="r">DNA to RNA (T to U)</option>
+		</param>
+	</inputs>
+
+    <!-- 
+    Functional tests with param value starting with - fail.
+     -->
+	<tests>
+		<test>
+			<param version="1.0.0" name="input" value="fasta_nuc_changer1.fasta" /> 
+			<param version="1.0.0" name="mode" value="r" /> 
+			<output version="1.0.0" name="output" file="fasta_nuc_change1.out" />
+		</test>
+		<test>
+			<param version="1.0.0" name="input" value="fasta_nuc_changer2.fasta" /> 
+			<param version="1.0.0" name="mode" value="d" /> 
+			<output version="1.0.0" name="output" file="fasta_nuc_change2.out" />
+		</test>
+	</tests>
+  
+	<outputs>
+		<data format="input" version="1.0.0" name="output" metadata_source="input" />
+	</outputs>
+
+<help>
+**What it does**
+
+This tool converts RNA FASTA files to DNA (and vice-versa).
+
+In **RNA-to-DNA** mode, U's are changed into T's.
+
+In **DNA-to-RNA** mode, T's are changed into U's.
+
+--------
+
+**Example**
+
+Input RNA FASTA file ( from Sanger's mirBase )::
+
+    >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+    UGAGGUAGUAGGUUGUAUAGUU
+    >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+    UCCCUGAGACCUCAAGUGUGA
+    >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+    UGGAAUGUAAAGAAGUAUGUA
+
+Output DNA FASTA file (with RNA-to-DNA mode)::
+
+    >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+    TGAGGTAGTAGGTTGTATAGTT
+    >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+    TCCCTGAGACCTCAAGTGTGA
+    >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+    TGGAATGTAAAGAAGTATGTA
+
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+ 
+</help>
+</tool>
diff -r 000000000000 -r 4b41e3076a50 test-data/fasta_nuc_change1.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_nuc_change1.out	Wed Sep 25 10:56:43 2013 -0400
@@ -0,0 +1,50 @@
+>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+UGAGGUAGUAGGUUGUAUAGUU
+>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+UCCCUGAGACCUCAAGUGUGA
+>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+UGGAAUGUAAAGAAGUAUGUA
+>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2
+UAUCACAGCCAGCUUUGAUGUGC
+>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34
+AGGCAGUGUGGUUAGCUGGUUG
+>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35
+UCACCGGGUGGAAACUAGCAGU
+>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36
+UCACCGGGUGAAAAUUCGCAUG
+>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37
+UCACCGGGUGAACACUUGCAGU
+>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38
+UCACCGGGAGAAAAACUGGAGU
+>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39
+UCACCGGGUGUAAAUCAGCUUG
+>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40
+UCACCGGGUGUACAUCAGCUAA
+>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41
+UCACCGGGUGAAAAAUCACCUA
+>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42
+UCACCGGGUUAACAUCUACAGA
+>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43
+UAUCACAGUUUACUUGCUGUCGC
+>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44
+UGACUAGAGACACAUUCAGCU
+>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45
+UGACUAGAGACACAUUCAGCU
+>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46
+UGUCAUGGAGUCGCUCUCUUCA
+>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47
+UGUCAUGGAGGCGCUCUCUUCA
+>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48
+UGAGGUAGGCUCAGUAGAUGCGA
+>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49
+AAGCACCACGAGAAGCUGCAGA
+>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50
+UGAUAUGUCUGGUAUUCUUGGG
+>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51
+UACCCGUAGCUCCUAUCCAUGUU
+>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52
+CACCCGUACAUAUGUUUCCGUGCU
+>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53
+CACCCGUACAUUUGUUUCCGUGCU
+>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54
+UACCCGUAAUCUUCAUAAUCCGAG
diff -r 000000000000 -r 4b41e3076a50 test-data/fasta_nuc_change2.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_nuc_change2.out	Wed Sep 25 10:56:43 2013 -0400
@@ -0,0 +1,50 @@
+>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+TGAGGTAGTAGGTTGTATAGTT
+>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+TCCCTGAGACCTCAAGTGTGA
+>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+TGGAATGTAAAGAAGTATGTA
+>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2
+TATCACAGCCAGCTTTGATGTGC
+>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34
+AGGCAGTGTGGTTAGCTGGTTG
+>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35
+TCACCGGGTGGAAACTAGCAGT
+>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36
+TCACCGGGTGAAAATTCGCATG
+>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37
+TCACCGGGTGAACACTTGCAGT
+>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38
+TCACCGGGAGAAAAACTGGAGT
+>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39
+TCACCGGGTGTAAATCAGCTTG
+>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40
+TCACCGGGTGTACATCAGCTAA
+>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41
+TCACCGGGTGAAAAATCACCTA
+>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42
+TCACCGGGTTAACATCTACAGA
+>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43
+TATCACAGTTTACTTGCTGTCGC
+>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44
+TGACTAGAGACACATTCAGCT
+>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45
+TGACTAGAGACACATTCAGCT
+>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46
+TGTCATGGAGTCGCTCTCTTCA
+>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47
+TGTCATGGAGGCGCTCTCTTCA
+>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48
+TGAGGTAGGCTCAGTAGATGCGA
+>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49
+AAGCACCACGAGAAGCTGCAGA
+>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50
+TGATATGTCTGGTATTCTTGGG
+>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51
+TACCCGTAGCTCCTATCCATGTT
+>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52
+CACCCGTACATATGTTTCCGTGCT
+>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53
+CACCCGTACATTTGTTTCCGTGCT
+>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54
+TACCCGTAATCTTCATAATCCGAG
diff -r 000000000000 -r 4b41e3076a50 test-data/fasta_nuc_changer1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_nuc_changer1.fasta	Wed Sep 25 10:56:43 2013 -0400
@@ -0,0 +1,50 @@
+>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+TGAGGTAGTAGGTTGTATAGTT
+>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+TCCCTGAGACCTCAAGTGTGA
+>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+TGGAATGTAAAGAAGTATGTA
+>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2
+TATCACAGCCAGCTTTGATGTGC
+>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34
+AGGCAGTGTGGTTAGCTGGTTG
+>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35
+TCACCGGGTGGAAACTAGCAGT
+>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36
+TCACCGGGTGAAAATTCGCATG
+>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37
+TCACCGGGTGAACACTTGCAGT
+>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38
+TCACCGGGAGAAAAACTGGAGT
+>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39
+TCACCGGGTGTAAATCAGCTTG
+>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40
+TCACCGGGTGTACATCAGCTAA
+>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41
+TCACCGGGTGAAAAATCACCTA
+>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42
+TCACCGGGTTAACATCTACAGA
+>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43
+TATCACAGTTTACTTGCTGTCGC
+>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44
+TGACTAGAGACACATTCAGCT
+>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45
+TGACTAGAGACACATTCAGCT
+>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46
+TGTCATGGAGTCGCTCTCTTCA
+>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47
+TGTCATGGAGGCGCTCTCTTCA
+>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48
+TGAGGTAGGCTCAGTAGATGCGA
+>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49
+AAGCACCACGAGAAGCTGCAGA
+>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50
+TGATATGTCTGGTATTCTTGGG
+>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51
+TACCCGTAGCTCCTATCCATGTT
+>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52
+CACCCGTACATATGTTTCCGTGCT
+>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53
+CACCCGTACATTTGTTTCCGTGCT
+>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54
+TACCCGTAATCTTCATAATCCGAG
diff -r 000000000000 -r 4b41e3076a50 test-data/fasta_nuc_changer2.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_nuc_changer2.fasta	Wed Sep 25 10:56:43 2013 -0400
@@ -0,0 +1,50 @@
+>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+UGAGGUAGUAGGUUGUAUAGUU
+>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+UCCCUGAGACCUCAAGUGUGA
+>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+UGGAAUGUAAAGAAGUAUGUA
+>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2
+UAUCACAGCCAGCUUUGAUGUGC
+>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34
+AGGCAGUGUGGUUAGCUGGUUG
+>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35
+UCACCGGGUGGAAACUAGCAGU
+>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36
+UCACCGGGUGAAAAUUCGCAUG
+>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37
+UCACCGGGUGAACACUUGCAGU
+>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38
+UCACCGGGAGAAAAACUGGAGU
+>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39
+UCACCGGGUGUAAAUCAGCUUG
+>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40
+UCACCGGGUGUACAUCAGCUAA
+>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41
+UCACCGGGUGAAAAAUCACCUA
+>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42
+UCACCGGGUUAACAUCUACAGA
+>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43
+UAUCACAGUUUACUUGCUGUCGC
+>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44
+UGACUAGAGACACAUUCAGCU
+>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45
+UGACUAGAGACACAUUCAGCU
+>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46
+UGUCAUGGAGUCGCUCUCUUCA
+>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47
+UGUCAUGGAGGCGCUCUCUUCA
+>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48
+UGAGGUAGGCUCAGUAGAUGCGA
+>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49
+AAGCACCACGAGAAGCUGCAGA
+>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50
+UGAUAUGUCUGGUAUUCUUGGG
+>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51
+UACCCGUAGCUCCUAUCCAUGUU
+>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52
+CACCCGUACAUAUGUUUCCGUGCU
+>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53
+CACCCGUACAUUUGUUUCCGUGCU
+>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54
+UACCCGUAAUCUUCAUAAUCCGAG
diff -r 000000000000 -r 4b41e3076a50 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 25 10:56:43 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>