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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 617026dab446713793b40d5556aac16180e68eea"
author artbio
date Wed, 26 May 2021 23:12:40 +0000
parents d727e7667fd3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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5
b76d5b9e9a15 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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1 <tool id="tarfast5" name="tarfast5" version="0.6.1">
0
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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2 <description></description>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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3 <requirements>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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4 <requirement type="package" version="2.6">pigz</requirement>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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5 <requirement type="package" version="1.34">tar</requirement>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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6 </requirements>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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7 <stdio>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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8 <exit_code range="1:" level="fatal" description="Tool exception" />
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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9 </stdio>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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10 <command detect_errors="exit_code"><![CDATA[
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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11 #for $file in $inputs:
4
d727e7667fd3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 249d82b663920626adc7d5300ffef43c065c1205"
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12 ln -s $file ${file.element_identifier}.fast5 &&
0
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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13 #end for
2
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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14 #if $output_format == "gzip":
1
39f340c72c4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 8bd895c48953189b94dbe095db8767b82187a491"
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15 export PIGZ="-p \${GALAXY_SLOTS:-4}" &&
4
d727e7667fd3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 249d82b663920626adc7d5300ffef43c065c1205"
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16 tar -cvh --use-compress-program=pigz -f $output *.fast5
2
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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17 #else:
4
d727e7667fd3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 249d82b663920626adc7d5300ffef43c065c1205"
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18 tar -cvh -f $output *.fast5
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c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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19 #end if
0
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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20 ]]></command>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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21 <inputs>
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d727e7667fd3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 249d82b663920626adc7d5300ffef43c065c1205"
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22 <param name="inputs" type="data" format="h5,fast5.tar" label="fast5 sequence files" multiple="true" />
2
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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23 <param name="output_format" type="select" label="compression of the tar archive" display="radio">
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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24 <option value="tar">tar (no compression)</option>
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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25 <option value="gzip" selected="true">tar.gz</option>
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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26 </param>
0
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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27 </inputs>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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28
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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29 <outputs>
2
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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30 <data format="fast5.tar" name="output" label="Archive of fast5" >
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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31 <change_format>
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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32 <when input="output_format" value="gzip" format="fast5.tar.gz"/>
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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33 </change_format>
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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34 </data>
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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35
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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36
0
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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37 </outputs>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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38
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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39 <tests>
2
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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40 <test> <!-- tar -->
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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41 <param name="inputs" value="F1.fast5.h5" ftype="h5" />
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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42 <param name="output_format" value="tar" />
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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43 <output file="archive.tar" name="output" compare="sim_size" delta="3000" />
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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44 </test>
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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45
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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46 <test> <!-- tar.gz -->
0
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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47 <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" />
2
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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48 <param name="output_format" value="gzip" />
c461e528dd9f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
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49 <output file="archive.tar.gz" name="output" compare="sim_size" delta="3000" />
0
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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50 </test>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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51 </tests>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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52 <help>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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53
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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54 **What it does**
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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55
5
b76d5b9e9a15 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 617026dab446713793b40d5556aac16180e68eea"
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56 Creates a fast5.tar or fast5.tar.gz archive of fast5 (h5) sequences files
0
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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57
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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58 .. class:: warningmark
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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59
5
b76d5b9e9a15 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 617026dab446713793b40d5556aac16180e68eea"
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60 This tools follows a "map-reduce" procedure: multiple inputs arranged as a
b76d5b9e9a15 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 617026dab446713793b40d5556aac16180e68eea"
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61 data collection are compressed into a single tar.gz archive.
0
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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62
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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63
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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64
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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65 **Output**
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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66
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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67 A fast5.tar.gz archive
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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68
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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69 </help>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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70
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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71 <citations>
5
b76d5b9e9a15 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 617026dab446713793b40d5556aac16180e68eea"
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72 <citation type="doi">10.11578/dc.20180330.1</citation>
0
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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73 </citations>
04ba0a8ac6cc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
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74 </tool>