Mercurial > repos > iuc > poretools_events

annotate poretools_events.xml @ 2:8621d14fa100 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:03:39 +0000
parents 28b11a08f348
children 0e62759b5e56
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9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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1 <?xml version="1.0"?>
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2 <tool id="poretools_events" name="Extract nanopore events" version="@VERSION@.1">
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9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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3 <description>from a set of sequencing reads</description>
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4 <expand macro="bio_tools"/>
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5 <macros>
9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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6 <import>macros.xml</import>
9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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7 </macros>
9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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8 <expand macro="requirements" />
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 poretools events $precalled '$input' > '$output'
9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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12 ]]>
9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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13 </command>
9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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14 <inputs>
9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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15 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
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16 <param name="precalled" argument="--pre-basecalled" type="boolean" truevalue="--pre-basecalled" falsevalue="" label="Report pre-basecalled events" />
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="tabular" />
9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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20 </outputs>
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21 <tests>
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22 <test>
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23 <expand macro="test_input" />
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24 <param name="precalled" value="false" />
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25 <output name="output" ftype="tabular">
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26 <assert_contents>
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27 <has_n_lines n="2901"/>
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28 <has_text text="template"/>
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29 <has_text text="complement"/>
28b11a08f348 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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30 <not_has_text text="pre_basecalled"/>
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31 </assert_contents>
28b11a08f348 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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32 </output>
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33 </test>
9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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34 <test>
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35 <expand macro="test_input" />
9a0daf9a81d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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36 <param name="precalled" value="true" />
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37 <output name="output" ftype="tabular">
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38 <assert_contents>
28b11a08f348 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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39 <has_n_lines n="3083"/>
28b11a08f348 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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40 <not_has_text text="template"/>
28b11a08f348 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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41 <not_has_text text="complement"/>
28b11a08f348 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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42 <has_text text="pre_basecalled"/>
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43 </assert_contents>
28b11a08f348 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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44 </output>
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45 </test>
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46 </tests>
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47 <help>
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48 Extract the raw nanopore events from each FAST5 file.
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49 </help>
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50 <expand macro="citations" />
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51 </tool>