Mercurial > repos > devteam > fasta_nucleotide_changer
changeset 0:4b41e3076a50
Uploaded tool tarball.
| author | devteam |
|---|---|
| date | Wed, 25 Sep 2013 10:56:43 -0400 |
| parents | |
| children | 2f868bfbe9de |
| files | fasta_nucleotide_changer.xml test-data/fasta_nuc_change1.out test-data/fasta_nuc_change2.out test-data/fasta_nuc_changer1.fasta test-data/fasta_nuc_changer2.fasta tool_dependencies.xml |
| diffstat | 6 files changed, 281 insertions(+), 0 deletions(-) [+] |
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--- /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>
--- /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
--- /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
--- /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
--- /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
--- /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>