Mercurial > repos > iuc > plasflow
annotate plasflow.xml @ 1:ea270d0ad0e6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
author | iuc |
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date | Sat, 21 Jan 2023 13:49:39 +0000 |
parents | bda6012394f7 |
children | 1d2a91ab28b7 |
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ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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1 <tool id="PlasFlow" name="PlasFlow" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> |
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bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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2 <description>Prediction of plasmid sequences in metagenomic contigs</description> |
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ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
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3 <macros> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
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4 <token name="@TOOL_VERSION@">1.1.0</token> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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5 <token name="@VERSION_SUFFIX@">0</token> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
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6 </macros> |
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bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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7 <requirements> |
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ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
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8 <requirement type="package" version="@TOOL_VERSION@">plasflow</requirement> |
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bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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9 </requirements> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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10 <command detect_errors="exit_code"><![CDATA[ |
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ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
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11 ## PlasFlow supports gz only partially |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
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12 ## https://github.com/smaegol/PlasFlow/blob/45604ff637c65f709dabff63e665fa60896be241/PlasFlow.py#L444 |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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13 #if $readFile.ext == "fasta.gz" |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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14 gunzip -c '$readFile' > 'reads.fasta' && |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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15 #else |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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16 ln -s '$readFile' 'reads.fasta' && |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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17 #end if |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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18 |
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bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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19 PlasFlow.py |
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ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
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20 --input 'reads.fasta' |
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bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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21 --output 'output' |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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22 --threshold '$threshold' |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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23 ]]></command> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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24 <inputs> |
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ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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25 <param name="readFile" type="data" format="fasta,fasta.gz" optional="true" label="Contig Sequences" /> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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26 <param argument="threshold" type="float" value="0.7" min="0" max="1" label="Threshold for probability filtering"/> |
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bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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27 </inputs> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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28 <outputs> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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29 <data name="probability_table" from_work_dir="output" format="tabular" label="${tool.name} on ${on_string}: Probability table" /> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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30 <data name="chromosomes" from_work_dir="output_chromosomes.fasta" format="fasta" label="${tool.name} on ${on_string}: Chromosomes" /> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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31 <data name="plasmids" from_work_dir="output_plasmids.fasta" format="fasta" label="${tool.name} on ${on_string}: Plasmids" /> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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32 <data name="unclassified" from_work_dir="output_unclassified.fasta" format="fasta" label="${tool.name} on ${on_string}: Unclassified" /> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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33 </outputs> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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34 <tests> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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35 <test> |
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ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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36 <param name="readFile" value="test.fasta" ftype="fasta"/> |
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bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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37 <param name="threshold" value="0.7"/> |
1
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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38 <output name="probability_table" value="output" compare="re_match"/> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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39 <output name="chromosomes" value="output_chromosomes.fasta"/> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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40 <output name="plasmids" value="output_plasmids.fasta"/> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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41 <output name="unclassified" value="output_unclassified.fasta"/> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
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42 </test> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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43 <test> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
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44 <param name="readFile" value="test.fasta.gz" ftype="fasta.gz"/> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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45 <param name="threshold" value="0.7"/> |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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46 <output name="probability_table" value="output" compare="re_match"/> |
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bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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47 <output name="chromosomes" value="output_chromosomes.fasta"/> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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48 <output name="plasmids" value="output_plasmids.fasta"/> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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49 <output name="unclassified" value="output_unclassified.fasta"/> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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50 </test> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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51 </tests> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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52 <help><![CDATA[ |
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ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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53 PlasFlow is a set of scripts used for prediction of plasmid sequences in |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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54 metagenomic contigs. It relies on the neural network models trained on full |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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55 genome and plasmid sequences and is able to differentiate between plasmids and |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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56 chromosomes with accuracy reaching 96%. It outperforms other available solutions |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
iuc
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57 for plasmids recovery from metagenomes and incorporates the thresholding which |
ea270d0ad0e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
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58 allows for exclusion of incertain predictions. |
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bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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59 ]]></help> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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60 <citations> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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61 <citation type="doi">10.1093/nar/gkx1321</citation> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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62 </citations> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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63 </tool> |
bda6012394f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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64 |