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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit f6cf3fc8a9446a0a591ad7e0e2d81101b42fc714
author iuc
date Mon, 18 Mar 2024 15:56:22 +0000
parents 18a46265455b
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cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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1 <tool id="red" name="Red" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
cc02b208f3a4 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>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
iuc
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3 <macros>
cc02b208f3a4 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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18a46265455b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit d0d15a68ae93d7557efcafaed75be750fec946a4
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5 <token name="@VERSION_SUFFIX@">1</token>
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cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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6 </macros>
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db57bc3b57af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit f6cf3fc8a9446a0a591ad7e0e2d81101b42fc714
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7 <xrefs>
db57bc3b57af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit f6cf3fc8a9446a0a591ad7e0e2d81101b42fc714
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8 <xref type="bio.tools">red</xref>
db57bc3b57af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit f6cf3fc8a9446a0a591ad7e0e2d81101b42fc714
iuc
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9 </xrefs>
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cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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10 <requirements>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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11 <requirement type="package" version="@TOOL_VERSION@">red</requirement>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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12 </requirements>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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13 <command detect_errors="exit_code"><![CDATA[
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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14 mkdir input output &&
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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16 ln -s '${input}' input/genome.fa &&
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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18 Red
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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19 -gnm input/
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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20 -msk output/
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18a46265455b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit d0d15a68ae93d7557efcafaed75be750fec946a4
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21 -rpt output/
18a46265455b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit d0d15a68ae93d7557efcafaed75be750fec946a4
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22 -frm 2
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cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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23 -cor \${GALAXY_SLOTS:-1}
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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24 ]]></command>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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25 <inputs>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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26 <param label="Genome sequence to mask" name="input" type="data" format="fasta" />
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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27 </inputs>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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28 <outputs>
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db57bc3b57af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit f6cf3fc8a9446a0a591ad7e0e2d81101b42fc714
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29 <data format="fasta" name="masked" label="${tool.name} on ${on_string}: masked genome" from_work_dir="output/genome.msk" />
db57bc3b57af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit f6cf3fc8a9446a0a591ad7e0e2d81101b42fc714
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30 <data format="bed" name="bed" label="${tool.name} on ${on_string}: bed" from_work_dir="output/genome.bed" />
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cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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31 </outputs>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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32 <tests>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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33 <test>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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34 <param name="input" value="small.fa" />
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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35 <output name="masked" file="small.msk" />
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18a46265455b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit d0d15a68ae93d7557efcafaed75be750fec946a4
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36 <output name="bed" file="small.bed" />
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cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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37 </test>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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38 </tests>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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39 <help><![CDATA[
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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40 This is Red (REpeat Detector) designed and developed by Hani Zakaria Girgis, PhD.
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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41
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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42 An intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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43 ]]></help>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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44 <citations>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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45 <citation type="doi">10.1186/s12859-015-0654-5</citation>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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46 </citations>
cc02b208f3a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/red commit 50b2be196f4df1bdbe47406613ef984ca32a2d7d
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47 </tool>