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annotate xpore_dataprep.xml @ 0:b64b9a2bf4f0 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
author artbio
date Wed, 26 May 2021 23:14:24 +0000
parents
children ff53cf0d0bbd
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b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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1 <tool id="xpore_dataprep" name="xpore-dataprep" version="0.5.6+galaxy1">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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2 <description></description>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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3 <requirements>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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4 <requirement type="package" version="0.5.6">xpore</requirement>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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5 <requirement type="package" version="1.9.0">pyensembl</requirement>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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6 </requirements>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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7 <stdio>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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8 <exit_code range="1:" level="fatal" description="Tool exception" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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9 </stdio>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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10 <command detect_errors="exit_code"><![CDATA[
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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11 xpore-dataprep
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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12 --eventalign '$eventalign_reads'
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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13 --summary '$eventalign_summary'
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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14 --out_dir out
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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15 --n_processes \${GALAXY_SLOTS:-4} &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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16 ls -la out
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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17 ]]></command>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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18 <inputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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19 <param name="eventalign_reads" type="data" format="txt,tabular" label="aligned nanopore events"
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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20 help="a nanopolish eventalign output that aligns the nanopore events to a reference" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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21 <param name="eventalign_summary" type="data" format="txt,tabular" label="nanopore eventalign summary"
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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22 help="a summary of nanopolish eventalign by read_name,read_index" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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23 </inputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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24
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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25 <outputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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26 <data format="txt" name="data_index" label="data.index" from_work_dir="./out/data.index" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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27 <data format="h5" name="eventalign_hdf5" label="eventalign.hdf5" from_work_dir="./out/eventalign.hdf5" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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28 <data format="txt" name="data_log" label="data.log" from_work_dir="./out/data.log" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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29 <data format="txt" name="eventalign_log" label="eventalign.log" from_work_dir="./out/eventalign.log" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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30 <data format="txt" name="data_readcount" label="data.readcount" from_work_dir="./out/data.readcount" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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31 <data format="json" name="data_json" label="data.json" from_work_dir="./out/data.json"/>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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32 </outputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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33
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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34 <tests>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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35 <test>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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36 <param name="eventalign_reads" value="dataprep_eventaligh_reads.tsv" ftype="tabular" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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37 <param name="eventalign_summary" value="dataprep_eventaligh_summary.tsv" ftype="tabular" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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38 <output file="data.index" name="data_index" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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39 <output file="data.log" name="data_log" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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40 <output file="eventalign.log" name="eventalign_log" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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41 <output file="data.readcount" name="data_readcount" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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42 <output file="data.json" name="data_json" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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43 <output file="eventalign.hdf5" name="eventalign_hdf5" compare="sim_size" delta="3000" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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44 </test>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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45 </tests>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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46 <help>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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47
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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48 **What it does**
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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49
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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50 Prepare data for differential analysis by xpore-diffmod analysis of differential RNA
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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51 modification across all tested positions.
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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52
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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53 .. class:: warningmark
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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54
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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55 In its current version, only preparation of data for analysis by xpore-diffmod based on a
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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56 **transcripts** collection reference is implemented.
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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57
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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58 **Inputs**
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59
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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60 This tools requires the following inputs::
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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61
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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62 - the "aligned nanopore events" file returned from nanopolish eventalign (also named squiggles)
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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63 - the "nanopolish summary" file also returned by nanopolish eventalign
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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64
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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65 **Outputs**
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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66
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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67 3 datasets that will be required by xpore-diffmod::
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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68
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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69 - data.index
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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70 - data.json
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71 - data.readcount
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72
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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73 plus 3 datasets not required by xpore-diffmod::
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74
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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75 - data.log
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76 - eventalign.hdf5
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77 - eventalign.log
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78
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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79 for details on xpore-data prep, see https://xpore.readthedocs.io/en/latest/index.html
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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80 and https://github.com/GoekeLab/xpore
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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81
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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82 </help>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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83
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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84 <citations>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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85 <citation type="doi">10.1101/2020.06.18.160010</citation>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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86 </citations>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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87 </tool>