Mercurial > repos > bgruening > rnaz
changeset 2:e5a88ce48e23 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit 74ad1c03418c837e304ed84087b97033c1ef77a2
author | bgruening |
---|---|
date | Mon, 24 Oct 2016 02:46:03 -0400 |
parents | f0465b3f1e43 |
children | 54229a841c63 |
files | rnaz.tar.bz2 rnaz.xml test-data/rnaz_input_trna.aln test-data/rnaz_result_trna.fasta tool_dependencies.xml |
diffstat | 5 files changed, 81 insertions(+), 38 deletions(-) [+] |
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--- a/rnaz.xml Thu Sep 17 16:50:15 2015 -0400 +++ b/rnaz.xml Mon Oct 24 02:46:03 2016 -0400 @@ -1,45 +1,54 @@ -<tool id="rnaz" name="RNAz" version="0.1.0"> +<tool id="rnaz" name="RNAz" version="2.1.0"> <description>predicting structurally conserved and thermodynamically stable RNA secondary structures</description> - <version_command>RNAz --version</version_command> + <requirements> <requirement type="package" version="2.1">rnaz</requirement> </requirements> + <stdio> <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> </stdio> + + <version_command>RNAz --version</version_command> <command> <![CDATA[ - RNAz $input - $forward - $reverse - $both_strands + RNAz '$input' + --$forward_or_reverse $dinucleotide $mononucleotide $locarnate - $no_shuffle - #if $cutoff_p != -1: - --cutoff=$cutoff_p + $noshuffle + #if $cutoff != -1.0: + --cutoff=$cutoff #end if - > temp.txt; - grep -v -E "^ |^#|^$" temp.txt > $outfile; - grep -E "^ |^#|^$" temp.txt; + > temp.txt && + grep -v -E "^ |^#|^$" temp.txt > '$outfile' && + grep -E "^ |^#|^$" temp.txt ]]> </command> <inputs> <param format="txt" name="input" type="data" label="Input Alignment File" /> - <param name="forward" type="boolean" checked="false" truevalue="--forward" falsevalue="" label="Score forward strand" help="--forward" /> - <param name="reverse" type="boolean" checked="false" truevalue="--reverse" falsevalue="" label="Score reverse strand" help="--reverse" /> - <param name="both_strands" type="boolean" checked="false" truevalue="-e" falsevalue="" label="Score both strands" help="-e" /> - <param name="cutoff_p" label="Probability cutoff" type="float" value="-1" help="-1 to deactivate"/> - <param name="dinucleotide" type="boolean" checked="true" truevalue="--dinucleotide" falsevalue="" label="Use dinucleotide shuffled z-scores" help="--dinucleotide" /> - <param name="mononucleotide" type="boolean" checked="true" truevalue="--mononucleotide" falsevalue="" label="Use mononucleotide shuffled z-scores" help="--mononucleotide" /> - <param name="locarnate" type="boolean" checked="false" truevalue="--locarnate" falsevalue="" label="Use decision model for structural alignments" help="--locarnate" /> - <param name="no_shuffle" type="boolean" checked="false" truevalue="--no-shuffle" falsevalue="" label="Never fall back to shuffling" help="--no-shuffle" /> + <param name="forward_or_reverse" type="select" label="Scored strand"> + <option value="forward">Score forward strand (-f)</option> + <option value="reverse">Score reverse strand (-r)</option> + <option value="both-strands">Score both strands (-b)</option> + </param> + <param argument="--cutoff" label="Probability cutoff" type="float" value="-1.0" help="-1.0 to deactivate"/> + <param argument="--dinucleotide" type="boolean" checked="true" truevalue="--dinucleotide" falsevalue="" label="Use dinucleotide shuffled z-scores" /> + <param argument="--mononucleotide" type="boolean" checked="true" truevalue="--mononucleotide" falsevalue="" label="Use mononucleotide shuffled z-scores" /> + <param argument="--locarnate" type="boolean" checked="false" truevalue="--locarnate" falsevalue="" label="Use decision model for structural alignments" /> + <param argument="--no-shuffle" name="noshuffle" type="boolean" checked="false" truevalue="--no-shuffle" falsevalue="" label="Never fall back to shuffling" /> </inputs> <outputs> <data name="outfile" format="fasta" /> </outputs> + <tests> + <test> + <param name="input" value="rnaz_input_trna.aln"/> + <output name="outfile" file="rnaz_result_trna.fasta"/> + </test> + </tests> <help> <![CDATA[ @@ -57,10 +66,14 @@ sacCer1 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC + sacKlu GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC + sacBay GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC + sacCas GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC - ** * * ** ** **** ** **** * *** ***** **** * ****** * + + \** * * \** \** \**\** \** \**\** * *\** \**\**\* *\**\* * \**\**\** * **Output** @@ -89,28 +102,43 @@ Prediction: OTHER - Result file: - - >sacCer1 +Result file: + +>sacCer1 + GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC + ..((((...((((........))))....(((((((((((....))))))))))))))). ( -19.00, z-score = -1.44, R) + >sacKlu + GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGC + ..((((...((((........))))....((((((((..(....)..)))))))))))). ( -16.00, z-score = -0.11, R) + >sacBay + GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC + ..((((...((((........))))....(((((((((((....))))))))))))))). ( -19.00, z-score = -1.44, R) + >sacCas + GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAAC + .((((((..((((........))))..............)))))).(((......))).. ( -12.69, z-score = 0.35, R) + >consensus + GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC + ..((((...((((........))))....(((((((((((....))))))))))))))). (-15.59 = -15.53 + -0.06) + ]]> </help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaz_input_trna.aln Mon Oct 24 02:46:03 2016 -0400 @@ -0,0 +1,14 @@ +CLUSTAL W (1.83) multiple sequence alignment + + +sacCer1 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC +sacBay GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC +sacKlu GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC +sacCas GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC + ** * * ** ** **** ** **** * *** ***** **** * ****** * + +sacCer1 CCCCTACAGGGCT +sacBay CCCCTACAGGGCT +sacKlu CCCCTACAGGGCT +sacCas CTCCCCTGGAGCA + * ** * **
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaz_result_trna.fasta Mon Oct 24 02:46:03 2016 -0400 @@ -0,0 +1,15 @@ +>sacCer1 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.74, R) +>sacBay +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.74, R) +>sacKlu +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.87, R) +>sacCas +GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA +(((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.36, R) +>consensus +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87)
--- a/tool_dependencies.xml Thu Sep 17 16:50:15 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -<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>