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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
author artbio
date Sun, 15 May 2022 15:11:49 +0000
parents ff53cf0d0bbd
children
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2
a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
artbio
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1 <tool id="xpore_dataprep" name="xpore-dataprep" version="2.1+galaxy0">
0
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"
artbio
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3 <requirements>
2
a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
artbio
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4 <requirement type="package" version="2.1">xpore</requirement>
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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5 </requirements>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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6 <stdio>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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7 <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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8 </stdio>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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9 <command detect_errors="exit_code"><![CDATA[
2
a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
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10 xpore dataprep
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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11 --eventalign '$eventalign_reads'
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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12 --out_dir out
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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13 --n_processes \${GALAXY_SLOTS:-4} &&
1
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
artbio
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14 mv ./out/data.index $data_index &&
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
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15 mv ./out/data.log $data_log &&
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a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
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16 mv ./out/eventalign.index $eventalign_index &&
1
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
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17 mv ./out/data.readcount $data_readcount &&
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
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18 mv ./out/data.json $data_json
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
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ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
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20
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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21 ]]></command>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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22 <inputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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23 <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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24 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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25 </inputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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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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27 <outputs>
1
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
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28 <data format="txt" name="data_index" label="data.index" />
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
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29 <data format="txt" name="data_log" label="data.log" />
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
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30 <data format="txt" name="data_readcount" label="data.readcount" />
2
a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
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31 <data format="txt" name="eventalign_index" label="eventalign.index" />
1
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
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32 <data format="json" name="data_json" label="data.json" />
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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33 </outputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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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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35 <tests>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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36 <test>
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_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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38 <output file="data.index" name="data_index" />
2
a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
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39 <output file="eventalign.index" name="eventalign_index" />
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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40 <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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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 </test>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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44 </tests>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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45 <help>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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46
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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47 **What it does**
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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48
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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49 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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50 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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51
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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52 .. class:: warningmark
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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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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54 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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55 **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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56
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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57 **Inputs**
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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58
2
a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
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59 This tools requires the following input::
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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60
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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61 - 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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62
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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63 **Outputs**
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 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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66
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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67 - data.index
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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68 - data.json
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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69 - data.readcount
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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70
2
a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
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71 plus 2 datasets not required by xpore-diffmod::
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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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 - data.log
2
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74 - eventalign.index
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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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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76 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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77 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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78
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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79 </help>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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80
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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81 <citations>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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82 <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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83 </citations>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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84 </tool>