annotate RM_custom_search.xml @ 30:cab41d23e2a3 draft

planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Thu, 03 Aug 2023 08:40:38 +0000
parents 58807b35777a
children 628b235d76c7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
1 <tool id="RMsearch2" name="RepeatMasker custom search2" version="1.0.3.3">
0
a4cd8608ef6b Uploaded
petr-novak
parents:
diff changeset
2
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
3 <description>Scan clustering results using RepeatMasker against custom database of
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
4 repeats
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
5 </description>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
6 <requirements>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
7 <requirement type="package" version="4.0.7">repeatmasker</requirement>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
8 <requirement type="package" version="3.6">python</requirement>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
9 <requirement type="package" version="2.3.2">r-r2html</requirement>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
10 <requirement type="package" version="2.54.0">bioconductor-biostrings</requirement>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
11 </requirements>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
12 <required_files>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
13 <include type="literal" path="RM_custom_search.py"/>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
14 <include type="literal" path="parallel.py"/>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
15 </required_files>
0
a4cd8608ef6b Uploaded
petr-novak
parents:
diff changeset
16
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
17
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
18 <command>
14
62fefa284036 Uploaded
petr-novak
parents: 13
diff changeset
19
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
20 python3 ${__tool_directory__}/RM_custom_search.py -i $input_zip -d $RMdatabase -g
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
21 $__root_dir__ -r $output_html;
0
a4cd8608ef6b Uploaded
petr-novak
parents:
diff changeset
22
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
23 </command>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
24
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
25 <inputs>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
26 <param format="zip" type="data" name="input_zip"
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
27 label="RepeatExplorer output data archive"
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
28 help="Zip archive obtained from previouse Graph-based sequence clustering"/>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
29 <param name="RMdatabase" format="fasta" type="data" label="Library of repeats"
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
30 help="Library of repeats as DNA sequences in fasta format. The recommended format for IDs in a custom library is : '>reapeatname#class/subclass'"/>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
31 </inputs>
0
a4cd8608ef6b Uploaded
petr-novak
parents:
diff changeset
32
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
33 <outputs>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
34 <data format="html" name="output_html"
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
35 label="HTML summary of custom database ${RMdatabase.hid} search on dataset ${input_zip.hid} "/>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
36 </outputs>
0
a4cd8608ef6b Uploaded
petr-novak
parents:
diff changeset
37
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
38 <help>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
39 **What it does**
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
40
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
41 Use this tool if you want to scan previous clustering result with custom database
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
42 of repeats using repeatmasker.
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
43
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 14
diff changeset
44 </help>
0
a4cd8608ef6b Uploaded
petr-novak
parents:
diff changeset
45 </tool>
a4cd8608ef6b Uploaded
petr-novak
parents:
diff changeset
46