annotate cluster_table2krona_format.xml @ 25:5dba804e6884 draft

planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 12:42:08 +0000
parents 58807b35777a
children cab41d23e2a3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 17
diff changeset
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">
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 17
diff changeset
2 <required_files>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 17
diff changeset
3 <include type="literal" path="cluster_table2krona_format.py"/>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 17
diff changeset
4 </required_files>
17
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 17
diff changeset
6 python '$__tool_directory__'/cluster_table2krona_format.py --input ${input} --output ${output}
17
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
7 #if $column == "Final_annotation"
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
8 -m
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
9 #end if
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
10 ]]></command>
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
11 <inputs>
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
12 <param type="data" name="input" format="txt" label="CLUSTER_table.csv" />
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
13 <param name="column" type="select" label="What annotation column do you want to include in the output?">
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
14 <option value="Final_annotation" >Final_annotation </option>
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
15 <option value="Automatic_annotation" selected="true" >Automatic_annotation </option>
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
16 </param>
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
17 </inputs>
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
18 <outputs>
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
19 <data format="tabular" name="output" label="RepeatExplorer cluster annotation formatted for Krona visualization from data ${input.hid}"/>
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
20 </outputs>/
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
21 <help><![CDATA[
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
22 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::
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
23
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
24
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
25 '"Number_of_reads_in_clusters" 3002 '
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
26 '"Number_of_clusters" 895 '
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
27 '"Number_of_superclusters" 895 '
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
28 '"Number_of_singlets" 6998 '
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
29 '"Number_of_analyzed_reads" 10000 '
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
30 '"Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation" "TAREAN_annotation" "Final_annotation"'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
31 '1 1 61 61 "All" "Other" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
32 '2 2 59 59 "All/repeat/satellite" "Putative satellites (high confidence)" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
33 '3 3 45 45 "All/repeat/satellite" "Putative satellites (low confidence)" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
34 '4 4 38 38 "All" "Other" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
35 '5 5 32 32 "All" "Other" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
36 '6 6 28 28 "All" "Other" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
37 '7 7 25 25 "All" "Other" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
38 '8 8 24 24 "All" "Other" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
39 '9 9 23 23 "All" "Other" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
40 '10 10 22 22 "All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre" "Other" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
41 '11 11 20 20 "All" "Other" ""'
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
42
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
43
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
44
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
45 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.
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
46
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
47 ]]></help>
d14b68e9fd1d Uploaded - new tools added
petr-novak
parents:
diff changeset
48 </tool>