Mercurial > repos > petr-novak > re_utils
annotate cluster_table2krona_format.xml @ 34:91996b991991 draft default tip
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author | petr-novak |
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date | Fri, 16 Feb 2024 15:22:21 +0000 |
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1 <tool id="cluster_table2krona_format" name="Convert RepeatExplorer2 CLUSTER_table.csv to Krona formatted input " version="1.0.0.3" python_template_version="3.5"> |
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2 <requirements> |
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3 <requirement type="package" version="3">python</requirement> |
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4 </requirements> |
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5 <required_files> |
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6 <include type="literal" path="cluster_table2krona_format.py"/> |
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7 </required_files> |
17 | 8 <command detect_errors="exit_code"><![CDATA[ |
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9 python '$__tool_directory__'/cluster_table2krona_format.py --input ${input} --output ${output} |
17 | 10 #if $column == "Final_annotation" |
11 -m | |
12 #end if | |
13 ]]></command> | |
14 <inputs> | |
15 <param type="data" name="input" format="txt" label="CLUSTER_table.csv" /> | |
16 <param name="column" type="select" label="What annotation column do you want to include in the output?"> | |
17 <option value="Final_annotation" >Final_annotation </option> | |
18 <option value="Automatic_annotation" selected="true" >Automatic_annotation </option> | |
19 </param> | |
20 </inputs> | |
21 <outputs> | |
22 <data format="tabular" name="output" label="RepeatExplorer cluster annotation formatted for Krona visualization from data ${input.hid}"/> | |
23 </outputs>/ | |
24 <help><![CDATA[ | |
25 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:: | |
26 | |
27 | |
28 '"Number_of_reads_in_clusters" 3002 ' | |
29 '"Number_of_clusters" 895 ' | |
30 '"Number_of_superclusters" 895 ' | |
31 '"Number_of_singlets" 6998 ' | |
32 '"Number_of_analyzed_reads" 10000 ' | |
33 '"Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation" "TAREAN_annotation" "Final_annotation"' | |
34 '1 1 61 61 "All" "Other" ""' | |
35 '2 2 59 59 "All/repeat/satellite" "Putative satellites (high confidence)" ""' | |
36 '3 3 45 45 "All/repeat/satellite" "Putative satellites (low confidence)" ""' | |
37 '4 4 38 38 "All" "Other" ""' | |
38 '5 5 32 32 "All" "Other" ""' | |
39 '6 6 28 28 "All" "Other" ""' | |
40 '7 7 25 25 "All" "Other" ""' | |
41 '8 8 24 24 "All" "Other" ""' | |
42 '9 9 23 23 "All" "Other" ""' | |
43 '10 10 22 22 "All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre" "Other" ""' | |
44 '11 11 20 20 "All" "Other" ""' | |
45 | |
46 | |
47 | |
48 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. | |
49 | |
50 ]]></help> | |
51 </tool> |