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annotate red.xml @ 1:611dbafcb095 draft default tip

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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 10:07:13 +0000
parents 7ce2085e6284
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
iuc
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1 <tool id="red" name="Red" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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2 <description>repeat masking</description>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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3 <macros>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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4 <token name="@TOOL_VERSION@">2018.09.10</token>
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611dbafcb095 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit d0d15a68ae93d7557efcafaed75be750fec946a4
iuc
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5 <token name="@VERSION_SUFFIX@">1</token>
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7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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6 </macros>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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7 <requirements>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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8 <requirement type="package" version="@TOOL_VERSION@">red</requirement>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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9 </requirements>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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10 <command detect_errors="exit_code"><![CDATA[
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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11 mkdir input output &&
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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12
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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13 ln -s '${input}' input/genome.fa &&
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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14
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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15 Red
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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16 -gnm input/
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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17 -msk output/
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611dbafcb095 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit d0d15a68ae93d7557efcafaed75be750fec946a4
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18 -rpt output/
611dbafcb095 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit d0d15a68ae93d7557efcafaed75be750fec946a4
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19 -frm 2
0
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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20 -cor \${GALAXY_SLOTS:-1}
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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21 ]]></command>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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22 <inputs>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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23 <param label="Genome sequence to mask" name="input" type="data" format="fasta" />
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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24 </inputs>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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25 <outputs>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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26 <data format="fasta" name="masked" from_work_dir="output/genome.msk" />
1
611dbafcb095 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit d0d15a68ae93d7557efcafaed75be750fec946a4
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27 <data format="bed" name="bed" from_work_dir="output/genome.bed" />
0
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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28 </outputs>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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29 <tests>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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30 <test>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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31 <param name="input" value="small.fa" />
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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32 <output name="masked" file="small.msk" />
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611dbafcb095 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit d0d15a68ae93d7557efcafaed75be750fec946a4
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33 <output name="bed" file="small.bed" />
0
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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34 </test>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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35 </tests>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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36 <help><![CDATA[
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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37 This is Red (REpeat Detector) designed and developed by Hani Zakaria Girgis, PhD.
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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38
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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39 An intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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40 ]]></help>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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41 <citations>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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42 <citation type="doi">10.1186/s12859-015-0654-5</citation>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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43 </citations>
7ce2085e6284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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44 </tool>