Mercurial > repos > iuc > schicexplorer_schicdemultiplex

comparison scHicDemultiplex.xml @ 1:649c86cedcb4 draft

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"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
comparison
equal deleted inserted replaced
0:e59d83af97a1 1:649c86cedcb4
17 --srrToSampleFile '$srrToSample' 17 --srrToSampleFile '$srrToSample'
18 --outputFolder outputFiles 18 --outputFolder outputFiles
19 --bufferSize $bufferSize 19 --bufferSize $bufferSize
20 --threads @THREADS@ 20 --threads @THREADS@
21 21
22 && cd outputFiles
23 && mkdir forward
24 && mkdir reverse
25 && mv *R1.fastq.gz forward
26 && mv *R2.fastq.gz reverse
27
22 ]]></command> 28 ]]></command>
23 <inputs> 29 <inputs>
24 30
25 <param name='fastq' type="data" format="fastq, fastq.gz" label="Raw fastq file from Nagano 2017."/> 31 <param name='fastq' type="data" format="fastq, fastq.gz" label="Raw fastq file from Nagano 2017."/>
26 <param name='barcodeFile' type="data" format="txt" label="barcode file" help="Use GSE94489_README.txt file "/> 32 <param name='barcodeFile' type="data" format="txt" label="barcode file" help="Use GSE94489_README.txt file "/>
27 <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."/> 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."/>
28 <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." /> 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." />
29 35
30 </inputs> 36 </inputs>
31 <outputs> 37 <outputs>
32 <collection name="outputFastqs" type="list" label="Demultiplexed fastq files"> 38 <collection name="outputFastqsForward" type="list" label="Demultiplexed fastq files: Forward">
33 <discover_datasets pattern="__name__" format="fastq.gz" directory="outputFiles" /> 39 <discover_datasets pattern="__name__" format="fastqsanger.gz" directory="outputFiles/forward" />
40 </collection>
41 <collection name="outputFastqsReverse" type="list" label="Demultiplexed fastq files: Reverse">
42 <discover_datasets pattern="__name__" format="fastqsanger.gz" directory="outputFiles/reverse" />
34 </collection> 43 </collection>
35 </outputs> 44 </outputs>
36 <tests> 45 <tests>
37 <test> 46 <test>
38 <param name='fastq' value='scHicDemultiplex/SRR5229025.fastq.gz' ftype="fastq.gz" /> 47 <param name='fastq' value='scHicDemultiplex/SRR5229025.fastq.gz' ftype="fastq.gz" />
39 <param name='barcodeFile' value='scHicDemultiplex/GSE94489_README.txt' /> 48 <param name='barcodeFile' value='scHicDemultiplex/GSE94489_README.txt' />
40 <param name='srrToSample' value='scHicDemultiplex/samples.txt' /> 49 <param name='srrToSample' value='scHicDemultiplex/samples.txt' />
41 <param name='bufferSize' value='1000' /> 50 <param name='bufferSize' value='1000' />
51 <output_collection name="outputFastqsForward" type="list" count="24">
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'/> -->
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'/>
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'/>
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'/> -->
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
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'/>
78 </output_collection>
42 79
43 80 <output_collection name="outputFastqsReverse" type="list" count="24">
44 <output_collection name="outputFastqs" type="list" count="48"> 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'/>
45 <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
46 <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
47 <element name="Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
48 <element name="Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
49 <element name="Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
50 <element name="Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
51 <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
52 <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
53 <element name="Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
54 <element name="Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
55 <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
56 <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
57 <element name="Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
58 <element name="Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
59 <element name="Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
60 <element name="Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
61 <element name="Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
62 <element name="Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
63 <element name="Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
64 <element name="Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
65 <element name="Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
66 <element name="Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
67 <element name="Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> 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'/>
68 <element name="Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
69 <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
70 <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
71 <element name="Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
72 <element name="Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
73 <element name="Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
74 <element name="Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
75 <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
76 <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
77 <element name="Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
78 <element name="Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
79 <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
80 <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
81 <element name="Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
82 <element name="Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
83 <element name="Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
84 <element name="Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
85 <element name="Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
86 <element name="Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
87 <element name="Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
88 <element name="Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
89 <element name="Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
90 <element name="Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
91 <element name="Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
92 <element name="Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/>
93 </output_collection> 105 </output_collection>
94 </test> 106 </test>
95 </tests> 107 </tests>
96 <help><![CDATA[ 108 <help><![CDATA[
97 109
98 Demultiplexing of raw fastq files 110 Demultiplexing of raw fastq files
99 ================================= 111 =================================
100 112
101 scHicDemultiplex demultiplexes fastq files from Nagano 2017: "Cell-cycle dynamics of chromosomal organization at single-cell resolution" according their barcodes to 113 scHicDemultiplex demultiplexes fastq files from Nagano 2017: "Cell-cycle dynamics of chromosomal organization at single-cell resolution" according their barcodes to
102 a seperated forward and reverse strand fastq files per cell. 114 a seperated forward and reverse strand fastq files per cell. For other datasets, a third-party demultiplexing strategy must be used.
115
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.
103 117
104 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ 118 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
105 119
106 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ 120 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
107 ]]></help> 121 ]]></help>