Mercurial > repos > iuc > red
comparison red.xml @ 0:cc02b208f3a4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
| author | iuc |
|---|---|
| date | Wed, 14 Sep 2022 12:02:55 +0000 |
| parents | |
| children | 18a46265455b |
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| -1:000000000000 | 0:cc02b208f3a4 |
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| 1 <tool id="red" name="Red" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | |
| 2 <description>repeat masking</description> | |
| 3 <macros> | |
| 4 <token name="@TOOL_VERSION@">2018.09.10</token> | |
| 5 <token name="@VERSION_SUFFIX@">0</token> | |
| 6 </macros> | |
| 7 <requirements> | |
| 8 <requirement type="package" version="@TOOL_VERSION@">red</requirement> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[ | |
| 11 mkdir input output && | |
| 12 | |
| 13 ln -s '${input}' input/genome.fa && | |
| 14 | |
| 15 Red | |
| 16 -gnm input/ | |
| 17 -msk output/ | |
| 18 -cor \${GALAXY_SLOTS:-1} | |
| 19 ]]></command> | |
| 20 <inputs> | |
| 21 <param label="Genome sequence to mask" name="input" type="data" format="fasta" /> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="fasta" name="masked" from_work_dir="output/genome.msk" /> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
| 28 <param name="input" value="small.fa" /> | |
| 29 <output name="masked" file="small.msk" /> | |
| 30 </test> | |
| 31 </tests> | |
| 32 <help><![CDATA[ | |
| 33 This is Red (REpeat Detector) designed and developed by Hani Zakaria Girgis, PhD. | |
| 34 | |
| 35 An intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. | |
| 36 ]]></help> | |
| 37 <citations> | |
| 38 <citation type="doi">10.1186/s12859-015-0654-5</citation> | |
| 39 </citations> | |
| 40 </tool> |