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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
author brinkmanlab
date Tue, 28 Jan 2020 15:33:51 -0500
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a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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1 <tool id="cheetah" name="Cheetah" version="1.0" profile="16.04">
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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2 <description>Generate reports using Galaxies built in Cheetah template engine and include information about datasets</description>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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3 <command><![CDATA[
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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4 mv $body $outfile
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5 ]]></command>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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6 <configfiles>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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7 <configfile name="body"><![CDATA[
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8 #set $template_path = '/'.join([$__tool_data_path__, "cheetah", $template])
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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9 #import os
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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10 #if '..' not in $template and $os.path.isfile($template_path)
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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11 #include $template_path
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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12 #else
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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13 <html>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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14 <body>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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15 $data.name is now complete.
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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16 #if $hasattr(__app__.config, "public_url")
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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17 You can view it <a href="${__app__.config.public_url}/datasets/${data.dataset.id}/display">here</a>.
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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18 #end if
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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19 </body>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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20 </html>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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21 #end if
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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22 ]]></configfile>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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23 </configfiles>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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24 <inputs>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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25 <param name="data" type="data" format="data" multiple="true" label="Data" />
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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26 <repeat name="extras" title="Extras">
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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27 <param name="extra" type="text" label="Extra data to make available in the template body" />
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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28 </repeat>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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29 <param name="template" type="text" value="template.html" label="Template" help="Relative path of template to use in tool-data/cheetah/" />
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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30 </inputs>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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31 <outputs>
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32 <data name="outfile" format="txt" />
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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33 </outputs>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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34 <help><![CDATA[
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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35 Generate reports using Galaxies built in Cheetah template engine and include information about datasets
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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36
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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37 Templates are parsed using Galaxies Cheeta Template Engine. The variables available are everything that is available to a tool including:
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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38 - $data Dataset instance passed to the tool input
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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39 - $extras[].extra List of extras specified in the tool parameters
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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40 - $template Relative path to the current template
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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41
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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42 See this tools xml for an example template.
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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43 ]]></help>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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44 <citations>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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45 <citation type="doi">10.5281/zenodo.3364789</citation>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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46 </citations>
a3bb4353fb00 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/cheetah commit e773feeb6feb9d533eef40ae5cead068e46f596e"
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47 </tool>