# HG changeset patch
# User bgruening
# Date 1477291563 14400
# Node ID e5a88ce48e23ccadafb86c7b548687ad93f2b6e8
# Parent  f0465b3f1e43ef2f4ad6ab39aef5115546576901
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit 74ad1c03418c837e304ed84087b97033c1ef77a2

diff -r f0465b3f1e43 -r e5a88ce48e23 rnaz.tar.bz2
Binary file rnaz.tar.bz2 has changed
diff -r f0465b3f1e43 -r e5a88ce48e23 rnaz.xml
--- 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>
diff -r f0465b3f1e43 -r e5a88ce48e23 test-data/rnaz_input_trna.aln
--- /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
+                * **    * ** 
diff -r f0465b3f1e43 -r e5a88ce48e23 test-data/rnaz_result_trna.fasta
--- /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) 
diff -r f0465b3f1e43 -r e5a88ce48e23 tool_dependencies.xml
--- 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>