17
+ − 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">
+ − 2 <command detect_errors="exit_code"><![CDATA[
+ − 3 $__tool_directory__/cluster_table2krona_format.py --input ${input} --output ${output}
+ − 4 #if $column == "Final_annotation"
+ − 5 -m
+ − 6 #end if
+ − 7 ]]></command>
+ − 8 <inputs>
+ − 9 <param type="data" name="input" format="txt" label="CLUSTER_table.csv" />
+ − 10 <param name="column" type="select" label="What annotation column do you want to include in the output?">
+ − 11 <option value="Final_annotation" >Final_annotation </option>
+ − 12 <option value="Automatic_annotation" selected="true" >Automatic_annotation </option>
+ − 13 </param>
+ − 14 </inputs>
+ − 15 <outputs>
+ − 16 <data format="tabular" name="output" label="RepeatExplorer cluster annotation formatted for Krona visualization from data ${input.hid}"/>
+ − 17 </outputs>/
+ − 18 <help><![CDATA[
+ − 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::
+ − 20
+ − 21
+ − 22 '"Number_of_reads_in_clusters" 3002 '
+ − 23 '"Number_of_clusters" 895 '
+ − 24 '"Number_of_superclusters" 895 '
+ − 25 '"Number_of_singlets" 6998 '
+ − 26 '"Number_of_analyzed_reads" 10000 '
+ − 27 '"Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation" "TAREAN_annotation" "Final_annotation"'
+ − 28 '1 1 61 61 "All" "Other" ""'
+ − 29 '2 2 59 59 "All/repeat/satellite" "Putative satellites (high confidence)" ""'
+ − 30 '3 3 45 45 "All/repeat/satellite" "Putative satellites (low confidence)" ""'
+ − 31 '4 4 38 38 "All" "Other" ""'
+ − 32 '5 5 32 32 "All" "Other" ""'
+ − 33 '6 6 28 28 "All" "Other" ""'
+ − 34 '7 7 25 25 "All" "Other" ""'
+ − 35 '8 8 24 24 "All" "Other" ""'
+ − 36 '9 9 23 23 "All" "Other" ""'
+ − 37 '10 10 22 22 "All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre" "Other" ""'
+ − 38 '11 11 20 20 "All" "Other" ""'
+ − 39
+ − 40
+ − 41
+ − 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.
+ − 43
+ − 44 ]]></help>
+ − 45 </tool>
