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comparison RM_custom_search.xml @ 22:58807b35777a draft

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planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 11:31:12 +0000
parents 62fefa284036
children 628b235d76c7
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21:f4ed6a65a2ff 22:58807b35777a
1 <tool id="RMsearch2" name="RepeatMasker custom search2" version="1.0.3"> 1 <tool id="RMsearch2" name="RepeatMasker custom search2" version="1.0.3.3">
2 2
3 <description>Scan clustering results using RepeatMasker against custom database of repeats</description> 3 <description>Scan clustering results using RepeatMasker against custom database of
4 <requirements> 4 repeats
5 <requirement type="package" version="4.0.7">repeatmasker</requirement> 5 </description>
6 <requirement type="package" version="3.6">python</requirement> 6 <requirements>
7 <requirement type="package" version="2.3.2">r-r2html</requirement> 7 <requirement type="package" version="4.0.7">repeatmasker</requirement>
8 <requirement type="package" version="2.54.0">bioconductor-biostrings</requirement> 8 <requirement type="package" version="3.6">python</requirement>
9 </requirements> 9 <requirement type="package" version="2.3.2">r-r2html</requirement>
10 <requirement type="package" version="2.54.0">bioconductor-biostrings</requirement>
11 </requirements>
12 <required_files>
13 <include type="literal" path="RM_custom_search.py"/>
14 <include type="literal" path="parallel.py"/>
15 </required_files>
10 16
11 <command>
12 17
13 python3 ${__tool_directory__}/RM_custom_search.py -i $input_zip -d $RMdatabase -g $__root_dir__ -r $output_html; 18 <command>
14 19
15 </command> 20 python3 ${__tool_directory__}/RM_custom_search.py -i $input_zip -d $RMdatabase -g
21 $__root_dir__ -r $output_html;
16 22
17 <inputs> 23 </command>
18 <param format="zip" type="data" name="input_zip" label="RepeatExplorer output data archive" help="Zip archive obtained from previouse Graph-based sequence clustering"/>
19 <param name="RMdatabase" format="fasta" type="data" label="Library of repeats" help="Library of repeats as DNA sequences in fasta format. The recommended format for IDs in a custom library is : '>reapeatname#class/subclass'"/>
20 </inputs>
21
22 <outputs>
23 <data format="html" name="output_html" label="HTML summary of custom database ${RMdatabase.hid} search on dataset ${input_zip.hid} " />
24 </outputs>
25 24
26 <help> 25 <inputs>
27 **What it does** 26 <param format="zip" type="data" name="input_zip"
27 label="RepeatExplorer output data archive"
28 help="Zip archive obtained from previouse Graph-based sequence clustering"/>
29 <param name="RMdatabase" format="fasta" type="data" label="Library of repeats"
30 help="Library of repeats as DNA sequences in fasta format. The recommended format for IDs in a custom library is : '>reapeatname#class/subclass'"/>
31 </inputs>
28 32
29 Use this tool if you want to scan previous clustering result with custom database of repeats using repeatmasker. 33 <outputs>
30 34 <data format="html" name="output_html"
31 </help> 35 label="HTML summary of custom database ${RMdatabase.hid} search on dataset ${input_zip.hid} "/>
36 </outputs>
37
38 <help>
39 **What it does**
40
41 Use this tool if you want to scan previous clustering result with custom database
42 of repeats using repeatmasker.
43
44 </help>
32 </tool> 45 </tool>
33 46