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comparison red.xml @ 1:18a46265455b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit d0d15a68ae93d7557efcafaed75be750fec946a4
author iuc
date Thu, 15 Sep 2022 10:07:47 +0000
parents cc02b208f3a4
children db57bc3b57af
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0:cc02b208f3a4 1:18a46265455b
1 <tool id="red" name="Red" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="red" name="Red" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>repeat masking</description> 2 <description>repeat masking</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2018.09.10</token> 4 <token name="@TOOL_VERSION@">2018.09.10</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">red</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">red</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
13 ln -s '${input}' input/genome.fa && 13 ln -s '${input}' input/genome.fa &&
14 14
15 Red 15 Red
16 -gnm input/ 16 -gnm input/
17 -msk output/ 17 -msk output/
18 -rpt output/
19 -frm 2
18 -cor \${GALAXY_SLOTS:-1} 20 -cor \${GALAXY_SLOTS:-1}
19 ]]></command> 21 ]]></command>
20 <inputs> 22 <inputs>
21 <param label="Genome sequence to mask" name="input" type="data" format="fasta" /> 23 <param label="Genome sequence to mask" name="input" type="data" format="fasta" />
22 </inputs> 24 </inputs>
23 <outputs> 25 <outputs>
24 <data format="fasta" name="masked" from_work_dir="output/genome.msk" /> 26 <data format="fasta" name="masked" from_work_dir="output/genome.msk" />
27 <data format="bed" name="bed" from_work_dir="output/genome.bed" />
25 </outputs> 28 </outputs>
26 <tests> 29 <tests>
27 <test> 30 <test>
28 <param name="input" value="small.fa" /> 31 <param name="input" value="small.fa" />
29 <output name="masked" file="small.msk" /> 32 <output name="masked" file="small.msk" />
33 <output name="bed" file="small.bed" />
30 </test> 34 </test>
31 </tests> 35 </tests>
32 <help><![CDATA[ 36 <help><![CDATA[
33 This is Red (REpeat Detector) designed and developed by Hani Zakaria Girgis, PhD. 37 This is Red (REpeat Detector) designed and developed by Hani Zakaria Girgis, PhD.
34 38