Mercurial > repos > bernhardlutz > rnaz

changeset 10:87f6ce525479 draft default tip

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Uploaded
author bernhardlutz
date Thu, 09 Jan 2014 16:11:17 -0500
parents c614f623f8f5
children
files rnaz.xml test-data/testfile.aln tool_dependencies.xml
diffstat 3 files changed, 99 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/rnaz.xml	Mon Dec 23 17:26:33 2013 -0500
+++ b/rnaz.xml	Thu Jan 09 16:11:17 2014 -0500
@@ -4,7 +4,7 @@
         <requirement type="package" version="2.1">rnaz</requirement>
     </requirements>
     <command>
-RNAz $inputaln $outfile
+RNAz $inputaln > $outfile
     </command>
     <stdio>
         <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
@@ -18,5 +18,9 @@
     </outputs>
     <help>**What it does**
      RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs.
+     
+     Gruber AR, Findeiss, Washietl S, Hofacker IL, and Stadler PF. 
+RNAz 2.0: Improved noncoding rna detection. 
+Pac Symp Biocomput, 2010. 15:69–79.
     </help>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testfile.aln	Thu Jan 09 16:11:17 2014 -0500
@@ -0,0 +1,80 @@
+CLUSTAL W(1.81) multiple sequence alignment
+
+hg17         T-GTGCTGAGTTGCCACAAAGTTGTCAAGTTACAATCCTTAG-ACATCACTGTAT---TC
+echTel1      T-GTGCTGAGTTGCCAGATAGTTGTCAAGGTACAGGCTGTAT-AGATCACCCTATCCTTC
+bosTau2      T-ATGCTGAGTTGCCACAAAGGTGTCATGTTACAATCCATAG-GCATCACTGTGTTGTTT
+canFam2      T-ATGCTGAATTGCCATACAGTTGTCAAGTTACAATCCTTAG-ACATCACTGTATTGCTT
+oryCun1      C-GTGCTGAGTTGCCATACAGTTGTCAAGTTGCAGTCCTTAG-ACATCACTGTGTTGTTC
+mm7          T-ATGCTGAATTG-CAGAACGTTGTCAAGGTATAATTTTTAG-ATATCACTATATGGCTC
+rn3          TGATGCTGAGTTG-TACAACGTTGTCAGGTTACAGTTTTTAG-ATATCACTACATAGCTG
+rheMac2      T-GTGCTGAGTTGCCACAAACTTGTCAAGTTAAAATCCTCAG-ACATCACTGTAT---TC
+panTro1      T-GTGCTGAGTTGCCACAAAGTTGTCAAGTTACAATCCTTAG-ACATCACTGTAT---TC
+monDom2      ----------------------TGGCAAGTCACAATCCTAAGTGTACCATTTTATCATTT
+
+hg17         TTGAGAGGCGTAGACCTGAGATGTGCTTATTTTTAGATTTAAACTTGATCAGCACTTGAT
+echTel1      TTGAGAGGAACACACCTTAGAGGAC-GTGTTTAGGACTGTAGG------CAGCACTTGAT
+bosTau2      CTGAGAGAAATAGACTCCAAATCTGCTTATTTAAGGATTTAGG------CAGCACTTGAT
+canFam2      CTGAGAGGAATAGACATAAGATGTGCTT-TTTAAGGATTTAGG------CAGCACTTGAT
+oryCun1      TTGACAGGAGTAGACCTGAGATGTGTATTTTTAAAGATGTAAACTTGGTCAGCACTTGAT
+mm7          TTATAAGGAGTGGGCCTGAGGGgtgtGTATTTAAGGATTTAGATTTGACCAGCACTTGAT
+rn3          TTA-AAGGAATGGGCCTGAGATGTGT---TTTAAGGATTTAGATGTGACCAGCACTTGAT
+rheMac2      TTGAGAGGTGTAGACCTGAGATGTGCTTATTTTTAGATTTAAACTTAATCAGCACTTGAT
+panTro1      TTGAGAGGCGTAGACCTGAGGTGTGCTTATTTTTAGATTTAAACTTGATCAGCACTTGAT
+monDom2      TTATTAGCAATAAGCCAAGACTGGTC----TTATCTATATGGAATTACCAAGCACTTGAT
+
+hg17         ACTAACCGAGCTGTCTATATCCTAGCCTTGTGTCAAAGGCTTGTGATGTG--TTGTGATA
+echTel1      ACTAACCGAGCTATCTATGTCCTAGCC-TATGTCAAAGGCTTGTGATGTG--TTGTGATC
+bosTau2      ACTAACCGAGCTATCTATGTCCAAGCCTTATGTCAGAGGCCTGTGATGTG--TTGTGATA
+canFam2      ACTAACCGAGCTATCTATATCCTAGCCTTGTGCCAAAGGCTTGTGATGTG--TTGTGATA
+oryCun1      ACTAACCGAGCTATCTGCATCCTGGTCTTGTGTCAAAGGCTTGGGATGTG--TTGTGATA
+mm7          ACTAACCGAGCTATCTGTATCCTCGTCTTGT-TTAAAGGCTTGTGATATG--CTGTGGTA
+rn3          ACTAACCGAGCTATCTATATCCTCGTCCTGT-CTAAAGGCTTG-GATATG--TTGTGATA
+rheMac2      ACTAACCTAGCTATCTATATCCTGGCTTTGTATCAAAGGCTTGTGATGTG--TTGTGATA
+panTro1      ACTAACCGAGCTGTCTGTATCCTAGCCTTGTGACAAAGGCTTGTGATGTG--TTGTGATA
+monDom2      ACTAACCAAGCTATCTGTATCCTGATGCCGCTCCAGAAG-TTGGGATGTATCTTGTGATA
+
+hg17         GCTGGGTTT-AAGAAGTGCAATATTAAAACAAAAGCCATGAGTCTTTTAAGCCCAGTGTG
+echTel1      GCTGGGTTT-AAGAAGTGCAATATTAAAAC--AAGCCATGAGTCTTTTAAGCCCAGGGTG
+bosTau2      GCTGGGTTT-AAGAAGTGCAATATTAAAACAAAAGCCATGAGTCTTTTAAGCCCAGGGTG
+canFam2      GCTGGGTTT-AAGAAGTGCAATATTAAAACAAAAGCCATGAGTCTTTTAAGCCCAGTGTG
+oryCun1      GCTGGGTTT-AAGAAGTGCAATATCAAAACAAAAGCCATGAGGCTTTTAAGCCCAGAGTG
+mm7          GTTGGGTTG-CAGAAGTGCGATATTAAAGTAAAAGCCATGAGTCTTTTAGGCCCAGTGTG
+rn3          GTTGGGTTG-CAGAAGTGCGATATTAAAGTCAAAGCCATGAGTCTTTTAGGCCCAGTGTG
+rheMac2      GCTGGGTTT-AAGAAGTGCAACATTAAAACAAAAGCCATGAGTCTTTTAAGCCCAGTGTG
+panTro1      GCTGGGTTT-AAGAAGTGCAATATTAAAACAAAAGCCATGAGTCTTTTAAGCCCAGTGTG
+monDom2      GCTGGGTTT-TATAAGTGCAATATTAAAGT--AAACCATGAGTCTTTTAAGCCCAGCATG
+
+hg17         TAAAGAT--ACACTCTGAGTTATAACTCAGAGGCACAAC-TGGATAGCAGT-------AC
+echTel1      TAAAGCC--ACACTCTGAGTTATAACTCAAAGGCACAAC-TGACTAGTGGC-------AC
+bosTau2      TAAAGAT--ACACTCTGAGTTATAACTCAGAGGCACAAC-TGGATAATGGT-------AT
+canFam2      TAAAGAC--ACACTCTGAGTTATAACTCAGAGGCACAAC-TGGATAGTGGT-------AT
+oryCun1      TAAAGAC--ACACTCTGAGTTATAACTCAGAGGCACAGC-TGGATAGTGGGATGCAGATT
+mm7          TAAAGAC--ACATTCTGAGTTATAACTCAGAGGCACATT-TGGATAGT----------AT
+rn3          TAAAGAC--ACACTCTGAGTTATAACTCAGAGGCACATT-TGGATAGTG---------AT
+rheMac2      TAAAGAT--ACACTCTGAGTTATAACTCAGAGGCACAAC-TGGATAGTGGT-------AC
+panTro1      TAAAGAT--ACACTCTGAGTTATAACTCAGAGGCACAAC-TGGATAGCGGT-------AC
+monDom2      TGGAGTTGAGCATGCTGGGTTATAACTCAAAGGTA------------CAGC-------AT
+
+hg17         TGGCCATAGCTAGTCAAGAAGCTACGGCTTTAGTGACT-GTTGAAAGCCAGTGCATTATT
+echTel1      TGGCCATATCAAGACAAGAAATTAAAGCTTTAGTGGCC-ATTGAAATCCAATGTGTTA--
+bosTau2      TAGCCATAGCTAGTTAAGCAGTTGCGGT-TTAGTGACTACTGAAGGGCCAGTGCATTATT
+canFam2      TAGCCATACCTAGTGAAGAAATTGTGGTGTTAGTGACT-TTTAAAGGCCAGTGCATTATT
+oryCun1      TAGTGACTGTTGGACTA-ATGCTTTAGTTCCTGCACTT-GG-ACAGAGCAGCACATTC-C
+mm7          CAGCAGTAGCCAGCCAC-AGGTCACAGCCTTGGGAACC-AG--AAGAACAAGGCACGA-T
+rn3          CAGCCGTGGCTAGCCAA-AAGTCACAGCCTTAGGAACC-AG-AAAGAACAAGGCATGA-T
+rheMac2      TGGCCATAGCTAGTCAAGAAGCTATGGCTTTAGTGACT-GTTGAAAGCCAGTGCATTATT
+panTro1      TGGCCATAGCTAGTCAAGAAGCTACGGCTTTAGTGACT-GTTGAAAGCCAGTGCATTATT
+monDom2      CGATGGTAGCCAGACCAGGAGTAATGACTATAATGAAA-ATCAGAAGCCAGT-------C
+
+hg17         TCATTCACTTGGA--CAGAAGCAGCACATTGTTCA
+echTel1      ---GTCATGTGGA--CAGAAGC---ACATTGTCCA
+bosTau2      TCATTCACCTGGA--CAGAAGAAGCAAATTGTCTT
+canFam2      TCATTCACTTG--------------ACATTGTTGA
+oryCun1      CTAAGCACAT-------------------------
+mm7          TCATTCAGTT-------------------------
+rn3          TCATTCACTT-------------------------
+rheMac2      TCAGTCACTTGGA--CAGAAGCAGCACATTGTTCA
+panTro1      TCATTCACTTGGA--CAGAAGCAGCACATTGTTCA
+monDom2      TCCTTGATATGAATTCAGATGTGAGATATT-CCCA
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jan 09 16:11:17 2014 -0500
@@ -0,0 +1,14 @@
+<tool_dependency>
+    <package name="rnaz" version="2.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://www.tbi.univie.ac.at/~wash/RNAz/RNAz-2.1.tar.gz</action>
+                <action type="autoconf" />
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling RNAz requires a C compiler (typically gcc)</readme>
+    </package>
+</tool_dependency>