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1 <tool id="cluster_table2krona_format" name="Convert RepeatExplorer2 CLUSTER_table.csv to Krona formatted input " version="1.0.0" python_template_version="3.5">
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2 <command detect_errors="exit_code"><![CDATA[
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3 $__tool_directory__/cluster_table2krona_format.py --input ${input} --output ${output}
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4 #if $column == "Final_annotation"
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5 -m
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6 #end if
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7 ]]></command>
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8 <inputs>
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9 <param type="data" name="input" format="txt" label="CLUSTER_table.csv" />
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10 <param name="column" type="select" label="What annotation column do you want to include in the output?">
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11 <option value="Final_annotation" >Final_annotation </option>
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12 <option value="Automatic_annotation" selected="true" >Automatic_annotation </option>
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13 </param>
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14 </inputs>
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15 <outputs>
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16 <data format="tabular" name="output" label="RepeatExplorer cluster annotation formatted for Krona visualization from data ${input.hid}"/>
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17 </outputs>/
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18 <help><![CDATA[
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19 This tool converts CLUSTER_table.csv RepeatExplorer2 output to file which can be visualized with Krona. As input use CLUSTER_table.csv obtained from RepeatExplorer2 analysis. Example of CLUSTER_table.csv::
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20
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21
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22 '"Number_of_reads_in_clusters" 3002 '
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23 '"Number_of_clusters" 895 '
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24 '"Number_of_superclusters" 895 '
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25 '"Number_of_singlets" 6998 '
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26 '"Number_of_analyzed_reads" 10000 '
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27 '"Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation" "TAREAN_annotation" "Final_annotation"'
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28 '1 1 61 61 "All" "Other" ""'
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29 '2 2 59 59 "All/repeat/satellite" "Putative satellites (high confidence)" ""'
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30 '3 3 45 45 "All/repeat/satellite" "Putative satellites (low confidence)" ""'
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31 '4 4 38 38 "All" "Other" ""'
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32 '5 5 32 32 "All" "Other" ""'
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33 '6 6 28 28 "All" "Other" ""'
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34 '7 7 25 25 "All" "Other" ""'
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35 '8 8 24 24 "All" "Other" ""'
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36 '9 9 23 23 "All" "Other" ""'
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37 '10 10 22 22 "All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre" "Other" ""'
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38 '11 11 20 20 "All" "Other" ""'
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39
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40
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41
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42 Last column "Final_annotation" is intended to be filled manually based on the curation of the automatic anotation results. If you obtain CLUSTER_table.csv directly from RepeatExplorer2 output, you can convert only automatic annotation table.
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43
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44 ]]></help>
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45 </tool>
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