diff rnazCluster.xml @ 0:d21d8e70e802 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnazCluster.xml	Wed Jan 30 04:14:06 2019 -0500
@@ -0,0 +1,61 @@
+<tool id="rnaz_cluster" name="RNAz Cluster" version="2.1">
+    <requirements>
+        <requirement type="package" version="2.1">rnaz</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    rnazCluster.pl
+    --cutoff $cutoff
+    $window_or_loci
+    #if $header:
+        $header
+    #end if
+    '$input'
+    > '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" format="text" />
+        <param argument="--cutoff" type="float" value="0.5" label="Only consider hits with RNAz class probality P>cutoff" />
+        <param name="window_or_loci" type="select" label="Print information for window or loci">
+            <option value="--windows">Print information for windows only</option>
+            <option value="--loci">Print information for loci only</option>
+        </param>
+        <param argument="--header" type="boolean" checked="true" truevalue="--header" falsevalue="" label="Print a header explaining the fields of the output" />
+    </inputs>
+    <outputs>
+        <data name="output" format="data"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="unknown.rnaz"/>
+            <param name="cutoff" value="0"/>
+            <output name="output" file="unknown.rnaz.clustered"/>
+        </test>
+        <test>
+            <param name="input" value="tRNA.rnaz"/>
+            <param name="window_or_loci" value="loci"/>
+            <output name="output" file="tRNA.rnaz.clustered"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    Clusters RNAz windows back into overlapping loci.
+
+    Usage: rnazCluster.pl [options] [file]
+
+    Options: -c X, --cutoff=X Only consider hits with RNAz class
+    probablility P > X (Default:0.5)
+
+    -w, --windows -l, --loci Set these flags to print information for
+    windows and/or loci in the output. By default, both single windows
+    and combined loci are printed.
+
+    -d, --header Print a header explaining the fields of the output
+    (see below for a detailed description of the fields).
+
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1142/9789814295291_0009</citation>
+    </citations>
+    
+</tool>