Mercurial > repos > iuc > schicexplorer_schicdemultiplex
annotate scHicDemultiplex.xml @ 1:649c86cedcb4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
| author | iuc |
|---|---|
| date | Tue, 10 Mar 2020 15:07:38 -0400 |
| parents | e59d83af97a1 |
| children | f224fc9af1d3 |
| rev | line source |
|---|---|
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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1 <tool id="schicexplorer_schicdemultiplex" name="@BINARY@" version="@WRAPPER_VERSION@.0"> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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2 <description>demultiplexes Nagano 2017 raw fastq files</description> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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3 <macros> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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4 <token name="@BINARY@">scHicDemultiplex</token> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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5 <import>macros.xml</import> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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6 </macros> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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7 <expand macro="requirements" /> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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9 #import re |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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10 mkdir outputFiles && |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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11 #set fastqFile = @ESCAPE_IDENTIFIER_FASTQ@ |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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12 ln -s '$fastq' '$fastqFile' && |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
changeset
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13 @BINARY@ |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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14 |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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15 --fastq $fastqFile |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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16 --barcodeFile '$barcodeFile' |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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17 --srrToSampleFile '$srrToSample' |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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18 --outputFolder outputFiles |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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19 --bufferSize $bufferSize |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
changeset
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20 --threads @THREADS@ |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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21 |
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1
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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22 && cd outputFiles |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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23 && mkdir forward |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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24 && mkdir reverse |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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25 && mv *R1.fastq.gz forward |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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changeset
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26 && mv *R2.fastq.gz reverse |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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27 |
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0
e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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28 ]]></command> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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29 <inputs> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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30 |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
changeset
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31 <param name='fastq' type="data" format="fastq, fastq.gz" label="Raw fastq file from Nagano 2017."/> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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32 <param name='barcodeFile' type="data" format="txt" label="barcode file" help="Use GSE94489_README.txt file "/> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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33 <param name='srrToSample' type="data" format="txt" label="SRR to Sample mapping file" help="The mappings from SRR number to sample id as given in the barcode file."/> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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34 <param name="bufferSize" type="integer" value="20000000" label="Buffer size" help="Number of lines to buffer in memory, if full, write the data to disk." /> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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35 |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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36 </inputs> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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37 <outputs> |
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1
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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38 <collection name="outputFastqsForward" type="list" label="Demultiplexed fastq files: Forward"> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
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39 <discover_datasets pattern="__name__" format="fastqsanger.gz" directory="outputFiles/forward" /> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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40 </collection> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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41 <collection name="outputFastqsReverse" type="list" label="Demultiplexed fastq files: Reverse"> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
diff
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42 <discover_datasets pattern="__name__" format="fastqsanger.gz" directory="outputFiles/reverse" /> |
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0
e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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43 </collection> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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44 </outputs> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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45 <tests> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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46 <test> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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47 <param name='fastq' value='scHicDemultiplex/SRR5229025.fastq.gz' ftype="fastq.gz" /> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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48 <param name='barcodeFile' value='scHicDemultiplex/GSE94489_README.txt' /> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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49 <param name='srrToSample' value='scHicDemultiplex/samples.txt' /> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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50 <param name='bufferSize' value='1000' /> |
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1
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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51 <output_collection name="outputFastqsForward" type="list" count="24"> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
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52 <!-- <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> --> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
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53 <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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54 <element name="Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
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55 <!-- <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> --> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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56 <element name="Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
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57 <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
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58 <element name="Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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59 <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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60 <element name="Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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61 <element name="Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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62 <element name="Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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63 <element name="Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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64 <element name="Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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65 <element name="Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
diff
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|
66 <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
diff
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|
67 <element name="Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
diff
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|
68 <element name="Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
diff
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|
69 <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
diff
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|
70 <element name="Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
diff
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|
71 <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
diff
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|
72 <element name="Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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|
73 <element name="Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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|
74 <element name="Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
diff
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|
75 <element name="Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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|
76 <element name="Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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|
77 <element name="Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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|
78 </output_collection> |
|
0
e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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79 |
|
1
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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|
80 <output_collection name="outputFastqsReverse" type="list" count="24"> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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81 <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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82 <element name="Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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83 <element name="Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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84 <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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85 <element name="Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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86 <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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87 <element name="Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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|
88 <element name="Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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89 <element name="Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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90 <element name="Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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91 <element name="Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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92 <element name="Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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93 <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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94 <element name="Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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95 <element name="Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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96 <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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97 <element name="Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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98 <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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99 <element name="Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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100 <element name="Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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101 <element name="Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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102 <element name="Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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103 <element name="Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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104 <element name="Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> |
|
0
e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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105 </output_collection> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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106 </test> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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107 </tests> |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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108 <help><![CDATA[ |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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109 |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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110 Demultiplexing of raw fastq files |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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111 ================================= |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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112 |
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e59d83af97a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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113 scHicDemultiplex demultiplexes fastq files from Nagano 2017: "Cell-cycle dynamics of chromosomal organization at single-cell resolution" according their barcodes to |
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1
649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
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114 a seperated forward and reverse strand fastq files per cell. For other datasets, a third-party demultiplexing strategy must be used. |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
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115 |
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649c86cedcb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
0
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116 Afterwards, the demultiplexed mapped data can be used with HiCExplorer `hicBuildMatrix` to create single cell .cool matrices that must be stored in a .scool file using `scHicMergeToSCool`, in order to be used for downstream analyses in the scHiCExplorer suite. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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117 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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118 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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119 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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120 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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121 ]]></help> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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122 <expand macro="citations" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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123 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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124 </tool> |