Mercurial > repos > iuc > poretools_stats

annotate poretools_stats.xml @ 1:4b17acf9b6ab draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
author iuc
date Sun, 19 Jan 2020 09:10:38 -0500
parents ae4c8446ce30
children c1cbe2575d32
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ae4c8446ce30 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"?>
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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2 <tool id="poretools_stats" name="Read length statistics" version="@VERSION@.0">
ae4c8446ce30 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 FAST5 files</description>
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4 <macros>
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5 <import>macros.xml</import>
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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6 </macros>
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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7 <expand macro="requirements" />
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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8 <command detect_errors="aggressive">
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9 <![CDATA[
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10 poretools stats --type $type $detailed '$input' > '$output'
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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11 ]]>
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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12 </command>
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13 <inputs>
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14 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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15 <param name="detailed" argument="--full-tsv" type="boolean" truevalue="--full-tsv" falsevalue="" label="Output detailed statistics" />
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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16 <expand macro="stat_options" />
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="tabular" />
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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" />
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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24 <param name="type" value="fwd" />
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25 <param name="detailed" value="true" />
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26 <output name="output" file="poretools-stats-out1.tabular" ftype="tabular" />
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27 </test>
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28 <test>
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29 <expand macro="test_input" />
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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30 <param name="type" value="rev" />
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31 <param name="detailed" value="false" />
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32 <output name="output" file="poretools-stats-out2.tabular" ftype="tabular" />
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33 </test>
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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34 <test>
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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35 <expand macro="test_input" />
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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36 <param name="type" value="2D" />
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37 <param name="detailed" value="true" />
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38 <output name="output" file="poretools-stats-out3.tabular" ftype="tabular" />
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39 </test>
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40 <test>
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41 <expand macro="test_input" />
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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42 <param name="type" value="best" />
ae4c8446ce30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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43 <param name="detailed" value="false" />
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44 <output name="output" file="poretools-stats-out4.tabular" ftype="tabular" />
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45 </test>
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46 <test>
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47 <expand macro="test_input" />
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48 <param name="type" value="all" />
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49 <param name="detailed" value="true" />
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50 <output name="output" file="poretools-stats-out5.tabular" ftype="tabular" />
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51 </test>
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52 </tests>
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53 <help>
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54 Collect read size statistics from a set of FAST5 files.
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55 </help>
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56 <expand macro="citations" />
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57 </tool>