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annotate rnazCluster.xml @ 0:dd08d42985fb draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
author bgruening
date Wed, 30 Jan 2019 03:58:47 -0500
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dd08d42985fb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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1 <tool id="rnaz_cluster" name="RNAz Cluster" version="2.1">
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2 <requirements>
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3 <requirement type="package" version="2.1">rnaz</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 rnazCluster.pl
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7 --cutoff $cutoff
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8 $window_or_loci
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9 #if $header:
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10 $header
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11 #end if
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12 '$input'
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13 > '$output'
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14 ]]></command>
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15 <inputs>
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16 <param type="data" name="input" format="text" />
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17 <param argument="--cutoff" type="float" value="0.5" label="Only consider hits with RNAz class probality P>cutoff" />
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18 <param name="window_or_loci" type="select" label="Print information for window or loci">
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19 <option value="--windows">Print information for windows only</option>
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20 <option value="--loci">Print information for loci only</option>
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21 </param>
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22 <param argument="--header" type="boolean" checked="true" truevalue="--header" falsevalue="" label="Print a header explaining the fields of the output" />
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="data"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input" value="unknown.rnaz"/>
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30 <param name="cutoff" value="0"/>
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31 <output name="output" file="unknown.rnaz.clustered"/>
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32 </test>
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33 <test>
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34 <param name="input" value="tRNA.rnaz"/>
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35 <param name="window_or_loci" value="loci"/>
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36 <output name="output" file="tRNA.rnaz.clustered"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40
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41 Clusters RNAz windows back into overlapping loci.
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42
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43 Usage: rnazCluster.pl [options] [file]
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44
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45 Options: -c X, --cutoff=X Only consider hits with RNAz class
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46 probablility P > X (Default:0.5)
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47
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48 -w, --windows -l, --loci Set these flags to print information for
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49 windows and/or loci in the output. By default, both single windows
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50 and combined loci are printed.
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51
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52 -d, --header Print a header explaining the fields of the output
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53 (see below for a detailed description of the fields).
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54
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55 ]]></help>
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56
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57 <citations>
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58 <citation type="doi">10.1142/9789814295291_0009</citation>
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59 </citations>
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60
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61 </tool>