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annotate clinker.xml @ 0:315f554107d7 draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
author thanhlv
date Thu, 21 Jul 2022 11:17:39 +0000
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315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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1 <tool id="clinker" name="clinker" version="@VERSION@+galaxy0">
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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2 <description> Automatic creation of publication-ready gene cluster comparison figures</description>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
thanhlv
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3 <macros>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
thanhlv
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4 <token name="@VERSION@">0.0.23</token>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
thanhlv
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5 </macros>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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6 <requirements>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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7 <requirement type="package" version="@VERSION@">clinker-py</requirement>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
thanhlv
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8 </requirements>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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9 <version_command>clinker --version</version_command>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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10 <command detect_errors="exit_code"><![CDATA[
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
thanhlv
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11 #import re
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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12 mkdir gbk &&
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
thanhlv
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13 #for $counter, $input in enumerate($gbk):
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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14 #set $_input_file = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier))
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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15 ln -sf '$input' 'gbk/${$_input_file}' &&
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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16 #end for
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
thanhlv
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17 clinker
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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18 $no_align
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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19 --identity $identity
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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20 --jobs \${GALAXY_SLOTS:-4}
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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21 -dl ","
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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22 -dc 4
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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23 #if $output
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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24 --output am.csv
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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25 #end if
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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26 gbk/*.gbk
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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27 -p plot.html
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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28 ]]> </command>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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29
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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30 <inputs>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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31 <param name="gbk" type="data" format="genbank" multiple="true" label="Genbank files"/>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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32 <param argument="no_align" type="boolean" truevalue="--no_align" falsevalue="" checked="false" label="Do not align clusters" />
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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33 <param argument="identity" type="float" min="0.1" value="0.3" max="1.0" label="Minimum alignment sequence identity" />
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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34 <param argument="output" type="boolean" truevalue="--output" falsevalue="" checked="false" label="Save alignments to file" />
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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35 </inputs>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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36 <outputs>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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37 <data name="alignment" format="txt" from_work_dir="am.csv" label="${tool.name} on ${on_string} Alignment file">
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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38 <filter>output is True</filter>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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39 </data>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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40 <data name="plot" format="html" from_work_dir="plot.html" label="${tool.name} on ${on_string} Plot" />
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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41 </outputs>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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42 <help><![CDATA[
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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43 Given a set of GenBank files, clinker will automatically extract protein translations, perform global alignments between sequences in each cluster, determine the optimal display order based on cluster similarity, and generate an interactive visualisation (using clustermap.js) that can be extensively tweaked before being exported as an SVG file.
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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44
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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45 See https://github.com/gamcil/clinker
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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46 ]]> </help>
315f554107d7 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/clinker commit 4987129d896224587be93815bcc0a6c050094820-dirty
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47 </tool>