Mercurial > repos > petr-novak > re_utils
comparison RM_custom_search.xml @ 14:62fefa284036 draft
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| author | petr-novak |
|---|---|
| date | Fri, 07 Feb 2020 06:06:47 -0500 |
| parents | f12eb3896842 |
| children | 58807b35777a |
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| 13:f12eb3896842 | 14:62fefa284036 |
|---|---|
| 1 <tool id="RMsearch" name="RepeatMasker custom search" version="1.0.3"> | 1 <tool id="RMsearch2" name="RepeatMasker custom search2" version="1.0.3"> |
| 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 repeats</description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="4.0.7">repeatmasker</requirement> | 5 <requirement type="package" version="4.0.7">repeatmasker</requirement> |
| 6 <requirement type="package">r-r2html</requirement> | 6 <requirement type="package" version="3.6">python</requirement> |
| 7 <requirement type="package">r-getopt</requirement> | 7 <requirement type="package" version="2.3.2">r-r2html</requirement> |
| 8 <requirement type="package">bioconductor-biostrings</requirement> | 8 <requirement type="package" version="2.54.0">bioconductor-biostrings</requirement> |
| 9 </requirements> | 9 </requirements> |
| 10 | 10 |
| 11 <command interpreter="python3"> | 11 <command> |
| 12 RM_custom_search.py -i $input_zip -d $RMdatabase -g $__root_dir__ -r $output_html | 12 |
| 13 python3 ${__tool_directory__}/RM_custom_search.py -i $input_zip -d $RMdatabase -g $__root_dir__ -r $output_html; | |
| 14 | |
| 13 </command> | 15 </command> |
| 14 | 16 |
| 15 <inputs> | 17 <inputs> |
| 16 <param format="zip" type="data" name="input_zip" label="RepeatExplorer output data archive" help="Zip archive obtained from previouse Graph-based sequence clustering"/> | 18 <param format="zip" type="data" name="input_zip" label="RepeatExplorer output data archive" help="Zip archive obtained from previouse Graph-based sequence clustering"/> |
| 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'"/> | 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'"/> |