12
|
1 <tool id="RMsearch" name="RepeatMasker custom search" version="1.0.3">
|
0
|
2
|
|
3 <description>Scan clustering results using RepeatMasker against custom database of repeats</description>
|
|
4 <requirements>
|
13
|
5 <requirement type="package" version="4.0.7">repeatmasker</requirement>
|
12
|
6 <requirement type="package">r-r2html</requirement>
|
|
7 <requirement type="package">r-getopt</requirement>
|
13
|
8 <requirement type="package">bioconductor-biostrings</requirement>
|
0
|
9 </requirements>
|
|
10
|
|
11 <command interpreter="python3">
|
|
12 RM_custom_search.py -i $input_zip -d $RMdatabase -g $__root_dir__ -r $output_html
|
|
13 </command>
|
|
14
|
|
15 <inputs>
|
9
|
16 <param format="zip" type="data" name="input_zip" label="RepeatExplorer output data archive" help="Zip archive obtained from previouse Graph-based sequence clustering"/>
|
0
|
17 <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'"/>
|
|
18 </inputs>
|
|
19
|
|
20 <outputs>
|
|
21 <data format="html" name="output_html" label="HTML summary of custom database ${RMdatabase.hid} search on dataset ${input_zip.hid} " />
|
|
22 </outputs>
|
|
23
|
|
24 <help>
|
|
25 **What it does**
|
|
26
|
|
27 Use this tool if you want to scan previous clustering result with custom database of repeats using repeatmasker.
|
|
28
|
|
29 </help>
|
|
30 </tool>
|
|
31
|